nod3.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright © 2012 MPIfR
# Peter Mueller
# contact: peter@mpifr.de
# Copyright © 2010-2011 CEA
# Pierre Raybaut
# Licensed under the terms of the CECILL License
# (see guiqwt/__init__.py for details)
"""
NOD3 single dish data reduction software
Image processing application on FITS data (NOD3FITS)
"""
import warnings
def fxn():
warnings.warn("deprecated", DeprecationWarning)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fxn()
import sys, platform, os.path as osp, os, re
import signal
import time
#try:
# import pywcs
#except:
# if hash('a') < 0:
# sys.path.append("/homes/peter/NOD3/32bit/lib/python2.6/site-packages")
# else:
# sys.path.append("/homes/peter/NOD3/64bit/lib/python2.6/site-packages")
if sys.path[0] == "": sys.path.pop(0)
if hash('a') < 0:
if sys.version_info[1] == 6:
sys.path.insert(1, sys.path[0]+"/32bit/lib/python2.6/site-packages")
else:
sys.path.insert(1, sys.path[0]+"/32bit/lib/python2.7/site-packages")
else:
if sys.version_info[1] == 6:
sys.path.insert(1, sys.path[0]+"/64bit/lib/python2.6/site-packages")
else:
sys.path.insert(1, sys.path[0]+"/64bit/lib/python2.7/site-packages")
NOD3DIR = os.getenv("HOME")
#NOD3DIR = os.getenv("HOME") + '/NOD3/Fits/'
NOD3_toolbar = ("EffRedu", "Processing", "Polarization", "Baseline", "MapEdit", "Filter", "Fit", "Misc", "Transform", "Galaxy", "Colors", "User")
from guidata.qt.QtGui import (QMainWindow, QMessageBox, QSplitter, QListWidget, qApp,
QVBoxLayout, QHBoxLayout, QWidget, QTabWidget,
QMenu, QApplication, QCursor, QFont, QColor, QFrame)
from guidata.qt.QtCore import Qt, QEvent, QObject, QT_VERSION_STR, PYQT_VERSION_STR, SIGNAL
from guidata.qt.QtGui import QPrinter, QPrintDialog, QPixmap
from guidata.qt.compat import getopenfilenames, getsavefilename
import guiqwt.colormap as cm
from guiqwt.curve import CurvePlot
from guiqwt.tools import (SelectPointTool, SelectTool, InteractiveTool, ColormapTool,
AnnotatedSegment, DefaultToolbarID, SegmentTool, CommandTool,
#ContrastPanelTool, CrossSectionTool, ItemListPanelTool,
ContrastPanelTool, ItemListPanelTool, AnnotatedSegmentTool,
AnnotatedRectangle, SaveAsTool, PrintTool, HelpTool, PrintFilter,
XCSPanelTool, YCSPanelTool, SnapshotTool, AspectRatioTool,
ReverseYAxisTool, RectangularActionTool, RectangularShapeTool,
AnnotatedEllipseTool, BaseCursorTool, ImageStatsTool)
import numpy as np
import copy as cp
import cPickle
from nod3tools import MapSelectTool, PolygonTool, ContrastTool, CrossSectionTool, TimeAxisTool
from guiqwt.image import pixelround, INTERP_NEAREST, INTERP_LINEAR
from guidata.dataset.datatypes import DataSet, ValueProp
from guidata.dataset.dataitems import (IntItem, FloatArrayItem, StringItem, TextItem,
ChoiceItem, FloatItem, DictItem, ButtonItem,
BoolItem)
from guidata.dataset.qtwidgets import DataSetEditGroupBox, DataSetEditLayout, FloatArrayWidget
from guidata.configtools import get_icon
from guidata.qthelpers import create_action, add_actions, get_std_icon
from guidata.qtwidgets import DockableWidget, DockableWidgetMixin
from guidata.utils import update_dataset, restore_dataset
from guiqwt.transitional import QwtLinearColorMap, QwtPlotPrintFilter
from guiqwt.config import CONF, _
from guiqwt.plot import ImageWidget, ImageDialog, CurveDialog
from guiqwt.builder import make
from guiqwt.signals import (SIG_LUT_CHANGED, SIG_CLICK_EVENT, SIG_ITEM_REMOVED,
SIG_VALIDATE_TOOL,
SIG_TOOL_JOB_FINISHED, SIG_AXIS_DIRECTION_CHANGED)
from guiqwt.events import (ClickHandler, QtDragHandler, ObjectHandler, KeyEventMatch,
MouseEventMatch, setup_standard_tool_filter)
from guiqwt.signals import (SIG_START_TRACKING, SIG_MOVE, SIG_STOP_NOT_MOVING, SIG_STOP_MOVING)
from guiqwt.styles import ItemParameters, ImageFilterParam, LabelParam
from guiqwt.image import ImageFilterItem
from guiqwt.geometry import (compute_center, compute_rect_size,
compute_distance, compute_angle)
from guiqwt.label import DataInfoLabel
from guiqwt.interfaces import IItemType
APP_NAME = _("NOD3 single dish data reduction system")
APP_DESC = _("""NOD3 is a data reduction and filtering tool<br>
with applications on FITS data""")
VERSION = '1.3.210'
from kapteyn import wcs
from nodmath import same_size, nanmean, nanmedian
directory = os.getenv("HOME") + "/Nod3Apps"
if not osp.exists(directory):
os.mkdir(directory)
def TimeDelta(val, typ):
'''returns h:m:s or d:m:s for axis labels'''
if val < 0:
val = -val
S = "-"
else:
S = ""
h = int(val/3600)
m = int((val-3600*h)/60)
s = int((val-3600*h-60*m))
if typ == "d":
ms = int(10*abs((val-3600*h-60*m) - s))
return "".join(["%s" % S, u"%2.2d°" % h, u"%2.2d'" % m, u'%2.2d.' % s, u'%1.1d"' % ms])
else:
ms = int(100*abs((val-3600*h-60*m) - s))
return "".join([u"%2.2d<sup>h</sup>" % h, "%2.2d<sup>m</sup>" % m, u"%2.2d." % s, '%2.2d<sup>s</sup>' % ms])
def nint(x):
if x > 0: return int(x+0.5)
else: return int(x-0.5)
def _add_all_supported_files(filters):
extlist = re.findall(r'\*.[a-zA-Z0-9]*', filters)
allfiles = '%s (%s)\n' % (_("All supported files"), ' '.join(extlist))
return allfiles+filters
class SignalParam(DataSet):
#FloatArrayItem.format_string
#title = StringItem(_("Title"), default=_("Untitled"))
#data = FloatArrayItem(_("Data"), transpose=True, minmax="both")
def copy_data_from(self, other, dtype=None):
self.xydata = np.array(other.xydata, copy=True, dtype=dtype)
def change_data_type(self, dtype):
self.xydata = np.array(self.xydata, dtype=dtype)
def get_data(self):
if self.xydata is not None:
return self.xydata[1]
def set_data(self, data):
self.xydata[1] = data
data = property(get_data, set_data)
def update_fits_metadata(obj):
# update new fits metadata from properties menu
for key in obj.metadata:
if type(key) == type(u'test'):
key = str(key)
if type(obj.metadata[key]) == type(u'test'):
obj.metadata[key] = str(obj.metadata[key])
obj.header[key] = obj.metadata[key]
class NOD3HelpTool(CommandTool):
def __init__(self, manager, toolbar_id=DefaultToolbarID):
super(NOD3HelpTool, self).__init__(manager, _("Help"),
get_std_icon("DialogHelpButton", 16),
toolbar_id=toolbar_id)
def activate_command(self, plot, checked):
"""Activate tool"""
QMessageBox.information(plot, _("Help"),
_("""Keyboard/mouse shortcuts:
- single left-click: item (curve, image, ...) selection
- single right-click: context-menu relative to selected item
- shift: on-active-curve (or image) cursor
- left-click + mouse move: move item (when available)
- middle-click + mouse move: pan
- right-click + mouse move: zoom
- Alt/Shift + mouse move: cursor and coordinates"""))
from guiqwt import pyplot
class NOD3SegmentTool(SegmentTool):
""" NOD3 patch to Segment tools"""
SWITCH_TO_DEFAULT_TOOL = False
#TITLE = _("Segment Tool")
TITLE = _("")
def __init__(self, manager, toolbar_id=DefaultToolbarID):
super(NOD3SegmentTool, self).__init__(manager, _("AnnotatedSegmentTool"),
tip=_("Segment Tool"), toolbar_id=toolbar_id)
self.default_tool = manager.get_default_tool()
self.setup_shape_cb = None
self.manager = manager
if not hasattr(self, 'annotation'):
self.annotation = AnnotatedSegment(0, 0, 1, 1)
self.annotation.get_rect = self.get_rect
self.rect = None
def erase(self):
self.manager.parent().imageft.clears_display()
if hasattr(self, 'fig'):
if self.fig.win != None:
if self.fig.win.isVisible():
self.manager.parent().imageft.fig.win.close()
del self.fig
def get_rect(self):
self.rect = self.annotation.shape.get_rect()
return self.annotation.shape.get_rect()
def create_plot(self):
item = self.manager.plot.get_active_item()
l1, b1, l2, b2 = self.rect
x1, y1 = item.get_pixel_coordinates(l1, b1)
x2, y2 = item.get_pixel_coordinates(l2, b2)
length = nint(np.hypot(x2-x1, y2-y1))
x, y = np.linspace(x1, x2, length), np.linspace(y1, y2, length)
z = item.data[y.astype(np.int), x.astype(np.int)]
l, b = np.linspace(l1, l2, length), np.linspace(b1, b2, length)
d = np.sqrt((l-l[0])**2 + (b-b[0])**2)
self.erase()
# plot it
self.fig = pyplot.figure("Segment-plot")
self.manager.parent().imageft.fig = self.fig
pyplot.plot(d, z, "b-")
pyplot.xlabel("Distance")
pyplot.ylabel("Data")
pyplot.zlabel("Segment plot")
pyplot.show(mainloop=False)
def create_shape(self):
self.annotation.annotationparam.show_label = False
if self.manager.plot.get_axis_unit(0) == "deg":
self.annotation.annotationparam.format = "%.4f"
else:
self.annotation.annotationparam.format = "%.1f"
self.set_shape_style(self.annotation)
self.default_tool.activate()
if self.rect != None:
x1, y1, x2, y2 = self.rect
self.create_plot()
return self.annotation, 0, 1
class NOD3FloatArrayWidget(FloatArrayWidget):
"""
FloatArrayItem widget
"""
def __init__(self, item, parent_layout):
super(NOD3FloatArrayWidget, self).__init__(item, parent_layout)
_label = item.get_prop_value("display", "label")
def update(self, arr):
"""Override AbstractDataSetWidget method"""
shape = arr.shape
if len(shape) == 1:
shape = (1,) + shape
dim = " x ".join( [ str(d) for d in shape ])
self.dim_label.setText(dim)
format = self.item.get_prop_value("display", "format")
minmax = self.item.get_prop_value("display", "minmax")
try:
if minmax == "all":
mint = format % np.nanmin(arr)
maxt = format % np.nanmax(arr)
elif minmax == "columns":
mint = ", ".join([format % np.nanmin(arr[r, :])
for r in range(arr.shape[0])])
maxt = ", ".join([format % np.nanmax(arr[r, :])
for r in range(arr.shape[0])])
else:
mint = ", ".join([format % np.nanmin(arr[:, r])
for r in range(arr.shape[1])])
maxt = ", ".join([format % np.nanmax(arr[:, r])
for r in range(arr.shape[1])])
except (TypeError, IndexError):
mint, maxt = "-", "-"
self.min_label.setText(mint)
self.max_label.setText(maxt)
class ImageParam(DataSet):
DataSetEditLayout.register(FloatArrayItem, NOD3FloatArrayWidget)
data = FloatArrayItem(_("Data (rows, cols)"), transpose=False, format="%.10g")
metadata = DictItem(_("Header"), default=None, help="Edit FITS header elements")
history = DictItem(_("NOD3 history"), default=None, help="Shows FITS history lines")
def copy_data_from(self, other, dtype=None):
self.data = np.array(other.data, copy=True, dtype=dtype)
if hasattr(other, 'header'):
# update new fits metadata from properties menu
update_fits_metadata(other)
self.header = other.header.copy()
if hasattr(other, 'parmap'):
self.parmap = np.array(other.parmap, copy=True, dtype=dtype)
if hasattr(other, 'sidmap'):
self.sidmap = np.array(other.sidmap, copy=True, dtype=dtype)
def change_data_type(self, dtype):
self.data = np.array(self.data, dtype=dtype)
class ObjectFT(QSplitter):
"""Object handling the item list, the selected item properties and plot"""
PARAMCLASS = None
PREFIX = None
def __init__(self, parent, plot):
super(ObjectFT, self).__init__(Qt.Vertical, parent)
self.Take = False
self.Pixel = False
self.Alpha = 1.0
self.AlphaMask = False
self.Outliers = 2.5
self.Separate = True
self.AxisUseHour = False
self.AxesUseTime = False
#self.InterpolationMode = INTERP_NEAREST
self.IntSize = None
self.plot = plot
self.objects = [] # signals or images
self.items = [] # associated plot items
self.listwidget = None
self.properties = None
self._hsplitter = None
self.file_actions = None
self.edit_actions = None
self.view_actions = None
self.operation_actions = None
self.processing_actions = None
self.baseline_actions = None
self.fit_actions = None
self.transform_actions = None
self.user_actions = None
self.imagewidget = parent.imagewidget
# Object selection dependent actions
self.actlist_1more = []
self.actlist_2more = []
self.actlist_1 = []
self.actlist_2 = []
# set grid invisible
if self.plot.grid.isVisible():
self.plot.grid.hide()
# keyboard interaction
self.KEY = None
self.STOP = False
self.original_sigint = signal.getsignal(signal.SIGINT)
signal.signal(signal.SIGINT, self.signal_handler)
# special patches to make life easier
self.plot.do_autoscale = self.do_autoscale
self.plot.do_zoom_view = self.do_zoom_view
self.plot.do_move_marker = self.do_move_marker
self.plot.cross_marker.update_label = self.update_label
self.plot.get_items = self.get_items
self.plot.Aspect = True
#self.plot.Aspect = False
a = 2.0*np.sqrt(2.0*np.log(2.0))
self.beam_norm = 2*np.pi / (a*a)
def keyPressEvent(self, event):
qApp.processEvents()
self.KEY = event.key()
#print self.KEY, '2'
if self.KEY == Qt.Key_C and (event.modifiers() & Qt.ControlModifier):
self.STOP = True
elif self.KEY == Qt.Key_Escape:
self.STOP = True
def Error(self, msg):
QMessageBox.critical(self.parent(), 'nod3',
_(u"Error:")+"\n%s" % str(msg))
def select(self):
self.item.selected = True
self.item.border_rect.unselect()
def get_items(self, z_sorted=False, item_type=None):
"""Return widget's item list
(items are based on IBasePlotItem's interface)"""
if z_sorted:
items = sorted(self.plot.items, reverse=False, key=lambda x:x.z())
else:
items = self.plot.items
if item_type is None:
return items
else:
assert issubclass(item_type, IItemType)
return [item for item in items if item_type in item.types()]
def do_zoom_view(self, dx, dy):
"""Reimplement CurvePlot method"""
CurvePlot.do_zoom_view(self.plot, dx, dy, lock_aspect_ratio=True)
def do_move_marker(self, event):
pos = event.pos()
self.plot.set_marker_axes()
if event.modifiers() & self.plot.curve_pointer:
self.plot.curve_marker.setZ(self.plot.get_max_z()+1)
self.plot.cross_marker.setVisible(False)
self.plot.curve_marker.setVisible(True)
self.plot.curve_marker.move_local_point_to(0, pos)
self.plot.replot()
#self.move_curve_marker(self.curve_marker, xc, yc)
elif event.modifiers() & Qt.ShiftModifier or self.plot.canvas_pointer:
self.ShiftModifier = True
self.plot.cross_marker.setZ(self.plot.get_max_z()+1)
self.plot.cross_marker.setVisible(True)
self.plot.curve_marker.setVisible(False)
self.plot.cross_marker.move_local_point_to(0, pos)
self.plot.replot()
#self.move_canvas_marker(self.cross_marker, xc, yc)
elif event.modifiers() & Qt.AltModifier or self.plot.canvas_pointer:
self.ShiftModifier = True
self.plot.cross_marker.setZ(self.plot.get_max_z()+1)
self.plot.cross_marker.setVisible(True)
self.plot.curve_marker.setVisible(False)
self.plot.cross_marker.move_local_point_to(0, pos)
self.plot.replot()
#self.move_canvas_marker(self.cross_marker, xc, yc)
else:
vis_cross = self.plot.cross_marker.isVisible()
vis_curve = self.plot.curve_marker.isVisible()
self.plot.cross_marker.setVisible(False)
self.plot.curve_marker.setVisible(False)
if vis_cross or vis_curve:
self.plot.replot()
def get_coordinates_label(self, xc, yc):
z = self.items[self.row].get_data(xc, yc)
return "x = %d<br>y = %d<br>z = %g" % (xc, yc, z)
def projection_xy(self, l, b, scale=True):
if self.nod3proj == None:
return l, b
xypixel = self.get_pixel_coordinates(l, b)
lp, bp = self.nod3proj.toworld(xypixel)
if scale:
return lp*self.vu, bp*self.vu
else:
return lp, bp
def update_label(self):
cm = self.plot.cross_marker
x1, y1 = cm.xValue(), cm.yValue()
if hasattr(self, 'ShiftModifier') and self.ShiftModifier:
x, y = self.projection_xy(x1, y1)
if not hasattr(self, 'row'):
return
xmin = min(self.items[self.row].xmin, self.items[self.row].xmax)
xmax = max(self.items[self.row].xmin, self.items[self.row].xmax)
ymin = min(self.items[self.row].ymin, self.items[self.row].ymax)
ymax = max(self.items[self.row].ymin, self.items[self.row].ymax)
if xmin <= x1 and xmax >= x1 and ymin <= y1 and ymax >= y1:
z = self.items[self.row].get_data(x1, y1)
else:
z = np.nan
if cm.label_cb:
label = cm.label_cb(x, y)
if label is None:
return
elif cm.is_vertical():
label = "x = %g" % x
elif cm.is_horizontal():
label = "y = %g" % y
elif self.Pixel:
label = u"x = %g<br>y = %g<br>z = %g" % (x, y, z)
elif not self.AxesUseTime:
label = u"x = %g°<br>y = %g°<br>z = %g" % (x, y, z)
else:
if self.AxisUseHour:
label = u"x = %s<br>y = %s<br>z = %g" % (TimeDelta(x/15.0, 'h'), TimeDelta(y, 'd'), z)
else:
label = u"x = %s<br>y = %s<br>z = %g" % (TimeDelta(x, 'd'), TimeDelta(y, 'd'), z)
text = cm.label()
text.setText(label)
cm.setLabel(text)
plot = cm.plot()
if plot is not None:
xaxis = plot.axisScaleDiv(cm.xAxis())
xmap = plot.canvasMap(cm.xAxis())
x_left, x_right = xmap.s1(), xmap.s2()
if x < (xaxis.upperBound()+xaxis.lowerBound())/2:
if x_left < x_right:
hor_alignment = Qt.AlignRight
else:
hor_alignment = Qt.AlignLeft
else:
if x_left < x_right:
hor_alignment = Qt.AlignLeft
else:
hor_alignment = Qt.AlignRight
yaxis = plot.axisScaleDiv(cm.yAxis())
ymap = plot.canvasMap(cm.yAxis())
y_top, y_bottom = ymap.s1(), ymap.s2()
if y < (yaxis.upperBound()+yaxis.lowerBound())/2:
if y_top > y_bottom:
ver_alignment = Qt.AlignBottom
else:
ver_alignment = Qt.AlignTop
else:
if y_top > y_bottom:
ver_alignment = Qt.AlignTop
else:
ver_alignment = Qt.AlignBottom
cm.setLabelAlignment(hor_alignment|ver_alignment)
def signal_handler(self, signum, frame):
self.STOP = True
#------Setup widget, menus, actions
def setup(self, toolbar):
self.listwidget = QListWidget()
#self.listwidget.setMinimumHeight(400)
self.listwidget.setAlternatingRowColors(True)
self.listwidget.setSelectionMode(QListWidget.ExtendedSelection)
self.properties = DataSetEditGroupBox(_("Properties"), self.PARAMCLASS)
self.properties.setEnabled(False)
self.connect(self.listwidget, SIGNAL("currentRowChanged(int)"),
self.current_item_changed)
self.connect(self.listwidget, SIGNAL("itemSelectionChanged()"),
self.selection_changed)
self.connect(self.properties, SIGNAL("apply_button_clicked()"),
self.properties_changed)
properties_stretched = QWidget()
properties_stretched.setMaximumHeight(260)
hlayout = QHBoxLayout()
hlayout.addWidget(self.properties)
#hlayout.addStretch()
vlayout = QVBoxLayout()
vlayout.addLayout(hlayout)
vlayout.addStretch()
properties_stretched.setLayout(vlayout)
self.addWidget(self.listwidget)
self.addWidget(properties_stretched)
# Edit actions
duplicate_action = create_action(self, _("Duplicate"),
icon=get_icon('copy.png'),
tip=_("Duplicate selected rows"),
triggered=self.duplicate_object)
self.actlist_1 += [duplicate_action]
createscript_action = create_action(self, _("CreateScript"),
icon=get_icon('edit.png'),
tip=_("Create script from history"),
triggered=self.create_script)
self.actlist_1 += [createscript_action]
remove_all_action = create_action(self, _("Remove ALL!"),
icon=get_icon('delete.png'),
tip=_("Remove all rows"),
triggered=self.remove_all_object)
#self.actlist_1 += [remove_all_action]
self.actlist_1more += [remove_all_action]
remove_action = create_action(self, _("Remove"),
icon=get_icon('delete.png'),
tip=_("Remove selected rows"),
triggered=self.remove_object)
self.actlist_1more += [remove_action]
self.edit_actions = [createscript_action, duplicate_action, remove_all_action, remove_action]
# Operation actions
sum_action = create_action(self, _("Sum"), triggered=self.compute_sum)
median_action = create_action(self, _("Median"),
triggered=self.compute_median)
average_action = create_action(self, _("Average"),
triggered=self.compute_average)
diff_action = create_action(self, _("Difference"),
triggered=self.compute_difference)
prod_action = create_action(self, _("Product"),
triggered=self.compute_product)
div_action = create_action(self, _("Division"),
triggered=self.compute_division)
self.actlist_2more += [sum_action, median_action, average_action, prod_action]
self.actlist_2 += [diff_action, div_action]
self.operation_actions = [sum_action, median_action, average_action,
diff_action, prod_action, div_action]
title_action = create_action(self, _("Set_Title"),
triggered=self.set_title)
limit_action = create_action(self, _("Plot_Limits"),
triggered=self.view_limits)
outlier_action = create_action(self, _("Plot_Outliers"),
triggered=self.view_outlier)
alpha_action = create_action(self, _("Plot_Transparency"),
triggered=self.view_alpha)
separate_action = create_action(self, _("Plot_Separate"),
triggered=self.view_separate)
format_action = create_action(self, _("Plot_Formats"),
triggered=self.view_plot_formats)
nearestpixel_action = create_action(self, _("NearestPixel"),
triggered=self.view_nearest_pixel)
interpolation_action = create_action(self, _("Linear Interpolation"),
triggered=self.view_interpolation)
pixel_action = create_action(self, _("Axes:Pixel"),
triggered=self.view_axes_pixel)
coordinate_action = create_action(self, _("Axes:Coordinates"),
triggered=self.view_axes_coordinate)
self.view_actions = [title_action, limit_action, outlier_action,
alpha_action, separate_action,
format_action, pixel_action, coordinate_action,
nearestpixel_action, interpolation_action]
#------GUI refresh/setup
def current_item_changed(self, row):
if row != -1:
update_dataset(self.properties.dataset, self.objects[row])
self.properties.get()
if hasattr(self, 'del_poly') and self.del_poly:
self.del_polygon()
else:
self.hide_polygon()
def _get_selected_rows(self):
return [index.row() for index in
self.listwidget.selectionModel().selectedRows()]
def selection_changed(self):
"""Signal list: selection changed"""
row = self.listwidget.currentRow()
self.properties.setDisabled(row == -1)
# reset to standard (default) tools
self._set_default_tools()
self.refresh_plot()
selected_rows = self._get_selected_rows()
nbrows = len(selected_rows)
for act in self.actlist_1more:
act.setEnabled(nbrows >= 1)
for act in self.actlist_2more:
act.setEnabled(nbrows >= 2)
for act in self.actlist_1:
act.setEnabled(nbrows == 1)
for act in self.actlist_2:
act.setEnabled(nbrows == 2)
# select items for colormaps
self.plot.selected_rows = []
for row in selected_rows:
item = self.items[row]
item.selected = True # is not self.item, item.select() will not work
self.plot.selected_rows.append(item)
def set_axis_coodinates(self, m):
self.vu = 1.0
if hasattr(m, 'header'):
self.has_coords = True
if 'SCANDIR' in m.header:
self.scandir = m.header['SCANDIR']
else:
self.scandir = "unknown"
B, L = m.data.shape
# corrects coordinates to pixel and plot
if self.InterpolationMode == INTERP_LINEAR:
off = 1.0
else:
off = 0.5
if self.scandir[:2] == "AL":
if "PATLONG" in m.header:
xoff = m.header['PATLONG']
else:
xoff = 0.0
if "PATLAT" in m.header:
yoff= m.header['PATLAT']
else:
yoff = 0.0
else:
xoff = yoff = 0.0
if "CUHPLONG" in m.header:
xoff = -m.header["CUHPLONG"]
if "CUHPLAT" in m.header:
yoff = m.header["CUHPLAT"]
l1 = (0-m.header['CRPIX1']+off)*m.header['CDELT1']
l2 = (L-m.header['CRPIX1']+off)*m.header['CDELT1']
b1 = (0-m.header['CRPIX2']+off)*m.header['CDELT2']
b2 = (B-m.header['CRPIX2']+off)*m.header['CDELT2']
#if m.header['CTYPE1'][-3:] == "DES" or m.header['CTYPE1'][-3:] == "XRC":
if "CTYPE1" in m.header and m.header['CTYPE1'][-3:] in ("CAR",):
self.descript = False
else:
self.descript = True
#if m.header['CTYPE1'].split("-")[0] == "RA" and self.scandir[:2] != "AL" \
# and not self.descript:
if self.descript:
fu = "deg"
#elif m.header['CTYPE2'][:3] in ("DEC", "LAT"):
#elif m.header['CTYPE2'][:3] == "DEC" and self.scandir != "ALON":
elif m.header['CTYPE2'][:3] == "DEC" and self.scandir[:2] != "AL":
fu = "hour"
else:
fu = "deg"
# set colorbar unit
if 'CALUNIT' in m.header:
m.header['BUNIT'] = m.header['CALUNIT']
del m.header['CALUNIT']
if 'BUNIT' in m.header:
calunit = m.header['BUNIT']
if calunit.find(" / ") < 0 and calunit.find("/") > 0:
calunit = calunit.replace("/", " / ")
self.plot.set_axis_title("right", calunit)
##self.plot.lock_aspect_ratio = self.Pixel
#self.plot.lock_aspect_ratio = self.plot.Aspect
if m.header['NAXIS1'] < m.header['NAXIS2']: self.plot.lock_aspect_ratio = False
#self.plot.apply_aspect_ratio()
Title = self.plot.get_axis_title("top")
self.plot.set_axis_title("top", Title)
self.plot.setTitle(Title)
self.plot.set_aspect_ratio(1.0, lock=True)
self.plot.apply_aspect_ratio()
if self.scandir[:2] == "AL":
self.plot.set_axis_title("bottom", "dAzimuth")
self.plot.set_axis_title("left", "dElevation")
elif m.header['CTYPE1'][:4] == "GLON":
self.plot.set_axis_title("bottom", "Galactic longitude")
self.plot.set_axis_title("left", "Galactic latitude")
#elif 'CROTA2' in m.header and m.header['CROTA2'] != 0.0:
elif 'CROTA2' in m.header and abs(m.header['CROTA2']) > 0.1:
self.plot.set_axis_title("bottom", "Longitude")
self.plot.set_axis_title("left", "Latitude")
elif self.descript:
self.plot.set_axis_title("bottom", "d"+m.header['CTYPE1'].split("-")[0])
self.plot.set_axis_title("left", "d"+m.header['CTYPE2'].split("-")[0])
else:
self.plot.set_axis_title("bottom", m.header['CTYPE1'].split("-")[0])
self.plot.set_axis_title("left", m.header['CTYPE2'].split("-")[0])
# change to Time Scale
#if m.header['CTYPE2'][:3] in ("DEC", "ALA", "LAT"):
if m.header['CTYPE2'][:3] in ("ALA", "LAT"):
self.AxesUseTime = True
self.AxisUseHour = False
elif m.header['CTYPE2'][:3] == "DEC":
self.AxesUseTime = True
self.AxisUseHour = True
else:
self.AxesUseTime = False
self.AxisUseHour = True
#if m.header['CTYPE1'].find("DES") > 0 or self.scandir[:2] == "AL":
if self.AxesUseTime:
self.plot.Unit = ' arcsec'
elif fu == "deg":
self.plot.Unit = " deg"
if self.Pixel:
self.plot.Unit = " pixel"
if self.descript or self.scandir[:2] == "AL":
if self.AxesUseTime:
vu = 3600.0
self.vu = vu
#self.plot.set_axis_unit("bottom", "d:m:s")
#self.plot.set_axis_unit("left", "d:m:s")
else:
if max(abs(l2-l1), abs(b2-b1)) > 1:
fu = "deg"
vu = 1.0
elif max(abs(l2-l1), abs(b2-b1)) > 0.02:
fu = "arcmin"
vu = 60.0
else:
fu = "arcsec"
vu = 3600.0
self.vu = vu
if "CTYPE1" in m.header and m.header['CTYPE1'][:2] == "GL":
self.plot.set_axis_unit("bottom", fu)
self.plot.set_axis_unit("left", fu)
else:
self.plot.set_axis_unit("bottom", None)
self.plot.set_axis_unit("left", None)
return l1*vu, l2*vu, b1*vu, b2*vu
elif m.header['CTYPE2'][:3] in ("DEC",):
l0 = m.header['CRVAL1']
b0 = m.header['CRVAL2']
vu = 3600.0
self.vu = vu
if 'EPOCH' in m.header:
if int(m.header['EPOCH']) == 2000: epoch = 'J2000'
elif int(m.header['EPOCH']) == 1950: epoch = 'B1950'
elif int(m.header['EPOCH']) == 1900: epoch = 'B1900'
else: epoch = "J"+str(int(m.header['EPOCH']))
self.AxisUseHour = True
self.plot.set_axis_unit("bottom", "%s" % epoch)
self.plot.set_axis_unit("left", "%s" % epoch)
else:
self.AxisUseHour = True
#return vu*((l1+l0)%360.0), vu*((l2+l0)%360.0), vu*(b1+b0), vu*(b2+b0)
return vu*((l1+l0)%360.0), vu*((l1+l0)%360.0 + l2-l1), vu*(b1+b0), vu*(b2+b0)
else:
l0 = m.header['CRVAL1']
b0 = m.header['CRVAL2']
if "CTYPE1" in m.header and m.header['CTYPE1'][:2] == "GL":
self.plot.set_axis_unit("bottom", fu)
self.plot.set_axis_unit("left", fu)
else:
self.plot.set_axis_unit("bottom", None)
self.plot.set_axis_unit("left", None)
self.vu = 1.0
return (l1+l0), (l2+l0), b1+b0, b2+b0
else:
self.has_coords = False
b2, l2 = m.data.shape
return 0, l2, 0, b2
def update_coordinates_projection(self, item):
phead = item.header.copy()
phead['NAXIS'] = 2
if "CTYPE1" in phead:
if phead['CTYPE1'][-3:] in ("DES", "SFL"):
phead['CRVAL1'] = 0.0
phead['CRVAL2'] = 0.0
if "CTYPE1" in phead:
phead['CTYPE1'] = phead['CTYPE1'].replace("DES", "CAR")
if "CTYPE2" in phead:
phead['CTYPE2'] = phead['CTYPE2'].replace("DES", "CAR")
if phead['CTYPE1'].find("CAR") > 0:
self.nod3proj = None
else:
self.nod3proj = wcs.Projection(phead)
def update_coordinates(self, item):
if self.Pixel or not 'CDELT1' in item.header:
self.nod3proj = None
else:
try: self.update_coordinates_projection(item)
except: pass
itemparams = ItemParameters(multiselection=True)
self.AxesUseTime = False
self.AxesUseHour = False
self.descript = False
#if self.Pixel or not 'CRVAL1' in item.header:
if self.Pixel or not 'CDELT1' in item.header:
# corrects coordinates to pixel and plot
if self.InterpolationMode == INTERP_LINEAR:
off = 0.5
else:
off = 0.0
self.plot.set_axis_title("left", 'Pixel')
self.plot.set_axis_unit("left", 'Pixel')
self.plot.set_axis_title("bottom", 'Pixel')
self.plot.set_axis_unit("bottom", 'Pixel')
irows, icols = item.data.shape
item.set_xdata(0+off, icols-1+off)
item.set_ydata(0+off, irows-1+off)
self.plot.set_axis_direction('bottom', reverse=False)
else:
l1, l2, b1, b2 = self.set_axis_coodinates(item)
item.set_xdata(l1, l2)
if item.header['CDELT1'] > 0.0:
self.plot.set_axis_direction('bottom', reverse=False)
else:
self.plot.set_axis_direction('bottom', reverse=True)
if item.header['CDELT2'] > 0.0:
self.plot.set_axis_direction('left', reverse=False)
else:
self.plot.set_axis_direction('left', reverse=True)
#if self.scandir[:2] == "AL":
# self.plot.set_axis_direction('bottom', reverse=False)
#else:
# self.plot.set_axis_direction('bottom', reverse=True)
item.set_ydata(b1, b2)
self.plot.AxesUseTime = self.AxesUseTime
self.plot.AxisUseHour = self.AxisUseHour
self.plot.Descript = False # never used with True
self.plot.NewPlot = True
item.update_bounds()
item.update_border()
#item.bounds = item.boundingRect()
item.get_item_parameters(itemparams)
item.set_item_parameters(itemparams)
#item.get_coordinates_label = self.get_coordinates_label
# reverse x-axis
#self.plot.set_axis_direction('bottom', reverse=True)
def set_NOD3_Title(self, m):
TITLE = ""
if 'TITLE' in m.header:
TITLE = m.header['TITLE']
elif hasattr(m, 'header'):
if 'OBJECT' in m.header:
#if 'OBJECT' in m.header:
TITLE = m.header['OBJECT']
if 'MAPTYPE' in m.header:
#if 'MAPTYPE' in m.header:
TITLE += str("[%s]" % m.header['MAPTYPE'])
if 'CRVAL3' in m.header:
#if 'CRVAL3' in m.header:
TITLE += str(" @ %-0.2f GHz" % (m.header['CRVAL3']*1.e-9))
if 'FILENAME' in m.header and 'SCANNUM' in m.header:
snum = int(m.header['SCANNUM'])
fname = m.header['FILENAME'].split("/")[-1]
TITLE += str(" # %4.4d %s" % (snum, fname))
elif 'FILENAME' in m.header:
fname = m.header['FILENAME'].split("/")[-1]
TITLE += str(" # %s" % (fname))
elif 'SCANNUM' in m.header:
#if 'SCANNUM' in m.header:
TITLE += str(" #%4.4d" % int(m.header['SCANNUM']))
self.plot.setTitle(TITLE)
self.plot.set_axis_title("top", TITLE)
def do_autoscale(self, replot=True):
"""Do autoscale on all axes"""
# XXX implement the case when axes are synchronised
vxmax = None
for axis_id in self.plot.AXIS_IDS:
vmin, vmax = None, None
if not self.plot.axisEnabled(axis_id):
continue
for item in self.plot.get_items():
if isinstance(item, self.plot.AUTOSCALE_TYPES) \
and not item.is_empty() and item.isVisible():
bounds = item.boundingRect()
if axis_id == item.xAxis():
xmin, xmax = bounds.left(), bounds.right()
if vmin is None or xmin < vmin:
vmin = xmin
if vmax is None or xmax > vmax:
vmax = xmax
elif axis_id == item.yAxis():
ymin, ymax = bounds.top(), bounds.bottom()
if vmin is None or ymin < vmin:
vmin = ymin
if vmax is None or ymax > vmax:
vmax = ymax
if vmin is None or vmax is None:
continue
if vmin == vmax: # same behavior as MATLAB
vmin -= 1
vmax += 1
elif vmin > 0 and vmax > 0: # log scale
vmin = 10**(np.log10(vmin))
vmax = 10**(np.log10(vmax))
if axis_id == item.xAxis():
vxmin = vmin
vxmax = vmax
step = -1
elif axis_id == item.yAxis():
vymin = vmin
vymax = vmax
step = 1
self.plot.set_axis_limits(axis_id, vmin, vmax, stepsize=step)
if vxmax != None: # and abs(vxmax-vxmin) < abs(vymax-vymin):
if abs(vxmax-vxmin) < abs(vymax-vymin):
ddx = ((vymax-vymin) - (vxmax-vxmin))/2.0
self.plot.set_axis_limits(item.xAxis(), vxmin-ddx, vxmax+ddx)
else:
ddy = ((vxmax-vxmin) - (vymax-vymin))/2.0
self.plot.set_axis_limits(item.yAxis(), vymin-ddy, vymax+ddy)
else:
return
self.plot.updateAxes()
self.emit(SIG_AXIS_DIRECTION_CHANGED, self, self.plot.get_axis_id(item.xAxis()))
self.emit(SIG_AXIS_DIRECTION_CHANGED, self, self.plot.get_axis_id(item.yAxis()))
if self.plot.lock_aspect_ratio:
self.plot.apply_aspect_ratio(full_scale=False)
if replot:
self.plot.replot()
def all_items(self):
for row in range(len(self.items)):
self.update_item(row)
def refresh_plot(self):
t=time.time()
for item in self.items:
if item is not None:
item.hide()
if hasattr(self, 'REMOVE'):
del self.REMOVE
return
for row in self._get_selected_rows():
# don't show all images on display, just the first
if row != self._get_selected_rows()[0]: break
self.row = row
item = self.items[row]
if item is None:
item = self.make_item(row)
# reset y-flip for NOD3 FITS images
#self.plot.set_axis_direction('left', False)
self.plot.add_item(item)
else:
self.update_item(row)
# don't show all images on display, just the first
if self._get_selected_rows()[0] == row:
self.plot.set_item_visible(item, True)
self.set_NOD3_Title(item)
# activates image on start
tx=time.time()
self.update_coordinates(item)
self.plot.set_active_item(item)
#self.plot.do_autoscale(replot=True)
self.do_autoscale(replot=True)
def _set_default_tools(self):
# reset cursor selecton
active_tool = self.imagewidget.get_active_tool()
if active_tool == self.get_tool(SelectPointTool):
if hasattr(self, 'cursor_activ'):
if self.cursor_activ:
QApplication.restoreOverrideCursor()
#QApplication.setOverrideCursor(QCursor(Qt.ArrowCursor))
self.selpos.end_callback = None
self.selpos.cursor = None
self.selpos.win.set_pointer(None)
self.selpos.deactivate()
self.cursor_activ = False
else:
self.cursor_activ = False
else:
# reset to SelectTool
self.imagewidget.set_default_tool = self.get_tool(SelectTool)
self.imagewidget.activate_default_tool()
# deactivate special tools:
Tools = ("CrossSectionTool", "ContrastPanelTool", "ImageStatsTool", "XCSPanelTool", "YCSPanelTool")
###for tool in self.imagewidget.tools:
for tool in Tools:
t = self.get_tool(eval(tool))
if hasattr(t, 'activate_command'):
t.activate_command(None, False)
# deactivate all other items but grid and image
item_list = []
for item in self.plot.items:
if str(item).find("curve.GridItem") < 0 and \
str(item).find("curve.PolygonMapItem") < 0 and \
str(item).find("image.ImageItem") < 0:
self.plot.del_item(item)
self.plot.emit(SIG_ITEM_REMOVED, item)
elif str(item).find("curve.GridItem") > 0:
self.griditem = item
def delete_item(self, my_item, new_current_row='current'):
for item in self.plot.items:
if str(item).find(my_item) > 0:
self.plot.del_items([item])
def refresh_list(self, new_current_row='current'):
"""new_current_row: integer, 'first', 'last', 'current'"""
# reset to standard (default) tools
self._set_default_tools()
row = self.listwidget.currentRow()
self.listwidget.clear()
self.listwidget.addItems(["%s%03d: %s" % (self.PREFIX, i+1, obj.title)
for i, obj in enumerate(self.objects)])
if new_current_row == 'first':
row = 0
elif new_current_row == 'last':
row = self.listwidget.count()-1
elif isinstance(new_current_row, int):
row = new_current_row
else:
assert new_current_row == 'current'
if row < self.listwidget.count():
self.listwidget.setCurrentRow(row)
# check for grid entry
if hasattr(self, 'griditem') and self.griditem in self.plot.items:
self.plot.del_items([self.griditem])
self.plot.add_item(self.griditem)
self.plot.replot()
def clears_display(self):
"""The properties 'Apply' button was clicked: updating signal"""
try:
self.hide_overlay = False
self.del_polygon()
row = self.listwidget.currentRow()
# update new fits metadata from properties menu
update_fits_metadata(self.objects[row])
# does not work with dummy (nan) check
update_dataset(self.objects[row], self.properties.dataset)
self.refresh_list(new_current_row='current')
self.listwidget.setCurrentRow(row)
#self.refresh_plot()
except:
pass
def properties_changed(self):
"""The properties 'Apply' button was clicked: updating signal"""
for i in range(2):
try:
self.hide_overlay = False
row = self.listwidget.currentRow()
# update new fits metadata from properties menu
update_fits_metadata(self.objects[row])
# does not work with dummy (nan) check
update_dataset(self.objects[row], self.properties.dataset)
self.refresh_list(new_current_row='current')
self.listwidget.setCurrentRow(row)
#self.refresh_plot()
self.hide_overlay = True
except:
pass
def add_object(self, obj):
if hasattr(obj, 'header'):
obj.metadata, obj.history = self.set_metadata(obj.header)
self.objects.append(obj)
self.items.append(None)
self.refresh_list(new_current_row='last')
self.listwidget.setCurrentRow(len(self.objects)-1)
self.emit(SIGNAL('object_added()'))
def replace_object(self, obj):
if hasattr(obj, 'header'):
obj.metadata, obj.history = self.set_metadata(obj.header)
self.objects.pop()
self.items.pop()
self.objects.append(obj)
self.items.append(None)
self.refresh_list(new_current_row='last')
self.listwidget.setCurrentRow(len(self.objects)-1)
self.emit(SIGNAL('object_replaced()'))
#------Edit operations
def duplicate_object(self):
rows = self._get_selected_rows()
if rows != []:
row = rows[0]
obj = self.objects[row]
objcopy = self.PARAMCLASS()
objcopy.title = obj.title
objcopy.copy_data_from(obj)
self.add_object(objcopy)
def create_script(self):
rows = self._get_selected_rows()
if rows != []:
row = rows[0]
obj = self.objects[row]
hlines = []
hcont = False
hist = []
append = False
if 'HISTORY' in obj.header:
for h in obj.header['HISTORY']:
h = str(h)
if h.find("NOD3:") >=0 or h.find("NOD3>") >=0:
hist.append(h)
if h.strip()[-1] == ")":
append = False
else:
append = True
elif append:
hist[-1] += h
for h in hist:
h = str(h)
if h.find("NOD3:") >=0:
hlines.append(h.split("NOD3:")[1])
if len(h) > 79: hcont = True
else: hcont = False
elif hcont:
hlines[-1] += h[8:].strip()
if len(h) > 79: hcont = True
else: hcont = False
if hlines == []:
import traceback
msg = "Sorry, no NOD3 history lines found in selected row "
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
else:
self.save_script(hlines)
def remove_all_object(self):
if self.Ask("Really remove ALL maps?"):
self.REMOVE = True
self.listwidget.selectAll()
self.remove_object()
def remove_object(self):
self.REMOVE = True
rows = sorted(self._get_selected_rows(), reverse=True)
row1 = max(rows[-1]-1, 0)
if rows != []:
for row in rows:
self.objects.pop(row)
item = self.items.pop(row)
self.plot.del_item(item)
#self.refresh_list(new_current_row='first')
#self.refresh_list(new_current_row='last')
#self.refresh_list(new_current_row='current')
self.refresh_list(new_current_row=row1)
self.refresh_plot()
#------Operations
def compute_sum(self):
rows = self._get_selected_rows()
sumobj = self.PARAMCLASS()
sumobj.title = "+".join(["%s%03d" % (self.PREFIX, row+1) for row in rows])
try:
for row in rows:
obj = self.objects[row]
if sumobj.data is None:
sumobj.copy_data_from(obj)
else:
sumobj.data += obj.data
#sumobj.data = np.nansum([sumobj.data, obj.data], axis=0)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
# write new history entry
sumobj.header.add_history("NOD3:"+sumobj.title)
self.add_object(sumobj)
def compute_median(self):
rows = self._get_selected_rows()
sumobj = self.PARAMCLASS()
title = ", ".join(["%s%03d" % (self.PREFIX, row+1) for row in rows])
sumobj.title = _("Median")+("(%s)" % title)
original_dtype = self.objects[rows[0]].data.dtype
objs = []
try:
for row in rows:
obj = self.objects[row]
if sumobj.data is None:
sumobj.copy_data_from(obj, dtype=np.float64)
objs.append(obj.data)
else:
#sumobj.data += obj.data
objs.append(obj.data)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
#sumobj.data /= float(len(rows))
try:
#sumobj.data = nanmedian(np.array(objs), axis=0)
sumobj.data = nanmedian(objs, axis=0)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
sumobj.change_data_type(dtype=original_dtype)
# write new history entry
sumobj.header.add_history("NOD3:"+str(sumobj.title))
self.add_object(sumobj)
def compute_average(self):
rows = self._get_selected_rows()
sumobj = self.PARAMCLASS()
title = ", ".join(["%s%03d" % (self.PREFIX, row+1) for row in rows])
sumobj.title = _("Average")+("(%s)" % title)
original_dtype = self.objects[rows[0]].data.dtype
objs = []
try:
for row in rows:
obj = self.objects[row]
if sumobj.data is None:
sumobj.copy_data_from(obj, dtype=np.float64)
objs.append(obj.data)
else:
#sumobj.data += obj.data
objs.append(obj.data)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
#sumobj.data /= float(len(rows))
try:
sumobj.data = nanmean(np.array(objs), axis=0)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
sumobj.change_data_type(dtype=original_dtype)
# write new history entry
sumobj.header.add_history("NOD3:"+str(sumobj.title))
self.add_object(sumobj)
def compute_average1(self):
from scipy import stats
rows = self._get_selected_rows()
sumobj = self.PARAMCLASS()
title = ", ".join(["%s%03d" % (self.PREFIX, row+1) for row in rows])
sumobj.title = _("Average")+("(%s)" % title)
original_dtype = self.objects[rows[0]].data.dtype
objs = []
try:
ms = []
for row in rows:
obj = self.objects[row]
ms.append(obj)
if sumobj.data is None:
sumobj.copy_data_from(obj, dtype=np.float64)
objs.append(obj.data)
else:
#sumobj.data += obj.data
objs.append(obj.data)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
sumobj.data /= float(len(rows))
try:
out, ms_new = same_size(ms)
if out > 0:
self.Error("one or more maps have different scales or coordinate systems")
return
data = []
for m in ms:
data.append(m.data)
sumobj.data = nanmean(data)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
sumobj.change_data_type(dtype=original_dtype)
# write new history entry
sumobj.header.add_history("NOD3:"+str(sumobj.title))
self.add_object(sumobj)
def compute_product(self):
rows = self._get_selected_rows()
sumobj = self.PARAMCLASS()
sumobj.title = "*".join(["%s%03d" % (self.PREFIX, row+1) for row in rows])
try:
for row in rows:
obj = self.objects[row]
if sumobj.data is None:
sumobj.copy_data_from(obj)
else:
sumobj.data *= obj.data
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
# write new history entry
sumobj.header.add_history("NOD3:"+sumobj.title)
self.add_object(sumobj)
def compute_difference(self):
rows = self._get_selected_rows()
diffobj = self.PARAMCLASS()
diffobj.title = "-".join(["%s%03d" % (self.PREFIX, row+1)
for row in rows])
try:
obj0, obj1 = self.objects[rows[0]], self.objects[rows[1]]
diffobj.copy_data_from(obj0)
diffobj.data = obj0.data-obj1.data
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
# write new history entry
diffobj.header.add_history("NOD3:"+diffobj.title)
self.add_object(diffobj)
def compute_division(self):
rows = self._get_selected_rows()
diffobj = self.PARAMCLASS()
diffobj.title = "/".join(["%s%03d" % (self.PREFIX, row+1)
for row in rows])
try:
obj0, obj1 = self.objects[rows[0]], self.objects[rows[1]]
diffobj.copy_data_from(obj0)
diffobj.data = obj0.data/obj1.data
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
# write new history entry
diffobj.header.add_history("NOD3:"+diffobj.title)
self.add_object(diffobj)
def view_alpha(self):
class AlphaParam(DataSet):
Alpha = FloatItem(_("Alpha"), default=1.0, min=0.0, max=1.0)
param = AlphaParam("Set transparency value", "alpha:")
param = self.read_defaults(param)
if not param.edit():
return
self.write_defaults(param)
self.Alpha = param.Alpha
if self.Alpha < 1.0:
self.AlphaMask = True
else:
self.AlphaMask = False
self.Take = False
self.Separate = False
self.refresh_plot()
def view_outlier(self, data):
class OutlierParam(DataSet):
Outliers = FloatItem(_("Outliers"), default=2.5)
param = OutlierParam("Set outliers", "Percent value:")
param = self.read_defaults(param)
if not param.edit():
return
self.write_defaults(param)
self.Outliers = param.Outliers
self.Take = False
self.Separate = False
self.refresh_plot()
def set_title(self):
class LimitParam(DataSet):
title = StringItem(_("Title:"), default="")
param = LimitParam("Set Title")
param = self.read_defaults(param)
if not param.edit():
return
self.write_defaults(param)
self.Title = param.title
try:
self.plot.setTitle(self.Title)
self.plot.set_axis_title("top", self.Title)
self.plot.refresh()
except:
pass
def view_limits(self):
dmin = 0.0
dmax = 1000.0
class LimitParam(DataSet):
Lower = FloatItem(_("Lower Limit"), default=dmin)
Upper = FloatItem(_("Upper Limit"), default=dmax)
#Take = BoolItem("Take", default=False)
param = LimitParam("Set plot range")
param = self.read_defaults(param)
param.Take = True
if not param.edit():
return
self.write_defaults(param)
self.Lower = param.Lower
self.Upper = param.Upper
self.Take = param.Take
self.Separate = False
self.refresh_plot()
def view_separate(self):
self.Separate = True
self.refresh_plot()
def view_plot_formats(self):
xformat = "%.3f"
yformat = "%.3f"
zformat = "%.3f"
class LimitParam(DataSet):
Xformat = StringItem(_("xformt"), default=xformat)
Yformat = StringItem(_("yformt"), default=yformat)
Zformat = StringItem(_("zformt"), default=zformat)
param = LimitParam("Set plot range")
param = self.read_defaults(param)
param.Take = True
if not param.edit():
return
self.write_defaults(param)
self.xformat = param.Xformat
self.yformat = param.Yformat
self.zformat = param.Zformat
self.all_items()
self.refresh_plot()
def view_nearest_pixel(self):
self.InterpolationMode = INTERP_NEAREST
self.IntSize = None
self.refresh_plot()
def view_interpolation(self):
self.InterpolationMode = INTERP_LINEAR
self.IntSize = None
self.refresh_plot()
def view_axes_coordinate(self):
self.Pixel = False
self.refresh_plot()
def view_axes_pixel(self):
self.Pixel = True
self.refresh_plot()
#------ROI selection
def func1(self, data):
return data.shape
def _roi_show(self, x, y, data, filter_area):
from scipy.ndimage import gaussian_filter
img = make.xyimage(x, y, data)
plot = self.imagewidget.get_plot()
xmin, xmax, ymin, ymax = filter_area
flt = make.imagefilter(xmin, xmax, ymin, ymax, img,
#filter=lambda x, y, data: gaussian_filter(data, 5))
filter=lambda x, y, data: gaussian_filter(data, 15))
#filter=lambda x, y, data: self.func(self.obj.data, self.obj.header, x, y))
#filter=self.func(self.obj.data, self.obj.header, x, y))
#filter=lambda x, y, data: self.func1(data))
plot.add_item(flt, z=1)
plot.set_active_item(flt)
plot.replot()
def roi_selection(self, name, func):
self.func = func
self.imagewidget.get_default_tool().deactivate()
row = self.listwidget.currentRow()
if row < 0: return
suffix = None
if row > -1:
self.image = self.items[row]
self.orig = self.objects[row]
self.obj = self.PARAMCLASS()
self.obj.title = "%s(%s%03d)" % (name, self.PREFIX, row+1)
if suffix is not None:
self.obj.title += " "+suffix(param)
title = str("%s(%s)" % (name, suffix(param)))
else:
title = str("%s()" % name)
self.obj.copy_data_from(self.orig)
self.obj.header = cp.copy(self.orig.header)
self.plot.unselect_all()
x = np.linspace(0, 30., self.obj.data.shape[1])
y = np.linspace(0, 30., self.obj.data.shape[0])
x0 = self.obj.data.shape[1]/2
y0 = self.obj.data.shape[0]/2
dx = int(x0/10.0)
dy = int(y0/10.0)
x1 = x0-dx
x2 = x0+dx
y1 = y0-dy
y2 = y0+dy
self._roi_show(x, y, self.obj.data, filter_area=(x1, x2, y1, y2))
def get_polyline(self, name, funct, param, addmap=True, onein=True):
row = self.listwidget.currentRow()
if row < 0: return
self.row = row
suffix = None
polyline = PolygonTool(self.plot.manager)
polyline.funct = funct
polyline.param = param
polyline.nextpoints = []
polyline._last_item = self.last_item
polyline.register_plot(self.plot)
polyline.activate()
polyline.setup_filter(self.plot)
if row == -1: return
self.objs = []
for row in self._get_selected_rows():
self.orig = self.objects[row]
self.obj = self.PARAMCLASS()
self.obj.title = "%s(%s%03d)" % (name, self.PREFIX, row+1)
if suffix is not None:
self.obj.title += " "+suffix(param)
title = str("%s(%s)" % (name, suffix(param)))
else:
title = str("%s()" % name)
self.obj.copy_data_from(self.orig)
self.objs.append(self.obj)
polyline.obj = self.objs[-1]
polyline.Finis = False
polyline.name = name
polyline.handle_input_output = self.handle_input_output
polyline.listwidget = self.listwidget
def get_box_positions(self, name, funct, param, nextbox=True, mshape="box", onein=True):
# close source list box if open
if hasattr(self, 'LView'):
if hasattr(self, 'N'): del self.N
if self.LView.isVisible():
self.LView.close()
# close pyplot figure if open
if hasattr(self, 'fig'):
if hasattr(self, 'N'): del self.N
try:
if self.fig.win.isVisible():
self.fig.win.close()
del self.fig
except: pass
row = self.listwidget.currentRow()
if row < 0: return
self.row = row
suffix = None
rect = MapSelectTool(self.plot.manager, shape_cb=mshape)
rect.ratio = 1.0
rect.funct = funct
rect.param = param
rect.nextbox = nextbox
rect.nextpos = []
rect._last_item = self.last_item
#dx = self.last_item.header['NAXIS1'] * self.last_item.header['CDELT1']/4
#dy = self.last_item.header['NAXIS2'] * self.last_item.header['CDELT2']/4
#rect.set_shape(0.0, 0.0, self.vu*abs(dx), self.vu*abs(dy))
#dx = self.last_item.header['NAXIS1']/5
#dy = self.last_item.header['NAXIS2']/5
dx, dy = 0.0, 0.0 # set to zero now 2015/11/10
rect.set_shape(0.0, 0.0, abs(dx), abs(dy))
rect.register_plot(self.plot)
rect.activate()
# activate <space> event because tool switches from MapSelectTool to SelectItem (???!)
rect.KeyEvent(parent=self.imagewidget.get_default_tool())
if row == -1: return
self.objs = []
for row in self._get_selected_rows():
self.orig = self.objects[row]
self.obj = self.PARAMCLASS()
self.obj.title = "%s(%s%03d)" % (name, self.PREFIX, row+1)
if suffix is not None:
self.obj.title += " "+suffix(param)
title = str("%s(%s)" % (name, suffix(param)))
else:
title = str("%s()" % name)
self.obj.copy_data_from(self.orig)
self.objs.append(self.obj)
rect.obj = self.objs[-1]
rect.objs = self.objs
rect.onein = onein
rect.Finis = False
rect.name = name
rect.handle_input_output = self.handle_input_output
rect.listwidget = self.listwidget
#------Cursor action
def get_tool(self, ToolKlass):
"""Return tool instance from its class"""
for tool in self.imagewidget.tools:
if isinstance(tool, ToolKlass):
return tool
def get_pixel_coordinates(self, l, b):
return self.items[self.row].get_pixel_coordinates(l, b)
def get_plot_coordinates(self, x, y):
# corrects coordinates to pixel and plot
if self.InterpolationMode == INTERP_LINEAR:
off = 0.0
else:
off = 0.5
l, b = self.items[self.row].get_plot_coordinates(x+off, y+off)
return l/self.vu, b/self.vu
def read_cursor(self, tool):
l, b = tool.get_coordinates()
x, y = self.get_pixel_coordinates(l, b)
self.func(self.objs, self.param, x, y)
self.cursor_activ = True
def _close_cursor(self, filter, event):
#print "cursor closed"
QApplication.restoreOverrideCursor()
self.plot.canvas_pointer = False
#QApplication.setOverrideCursor(QCursor(Qt.ArrowCursor))
if hasattr(self, 'selpos'):
self.selpos.end_callback = None
#self.selpos.cursor = None
#self.selpos.win.set_pointer(None)
#self.selpos.deactivate()
del self.selpos
self.cursor_activ = False
self.imagewidget.set_default_tool = self.get_tool(SelectTool)
self.imagewidget.activate_default_tool()
def Ask(self, msg):
ask = QMessageBox.question(self.parent(), 'NOD3', msg,
QMessageBox.Yes, QMessageBox.No)
if ask == QMessageBox.Yes: return True
else: return False
def get_cursor_positions(self, name, func, param, addmap=False, onein=True):
self.func = func
self.param = param
row = self.listwidget.currentRow()
if row < 0: return
self.row = row
suffix = None
QApplication.setOverrideCursor(QCursor(Qt.CrossCursor))
#QApplication.setOverrideCursor(QCursor(Qt.BlankCursor))
self.selpos = self.get_tool(SelectPointTool)
self.selpos.TITLE = name
self.selpos.TIP = "click on left button"
self.selpos.mode = "reuse"
self.selpos.marker = self.plot.cross_marker
self.selpos.end_callback = self.read_cursor
self.selpos.activate()
self.setup_KeyEvent(self.selpos, 'Cursor')
if hasattr(self.selpos, 'get_active_plot'):
self.selpos.win = self.selpos.get_active_plot()
self.selpos.win.set_pointer("canvas")
if row == -1: return
self.objs = []
for row in self._get_selected_rows():
self.orig = self.objects[row]
self.obj = self.PARAMCLASS()
self.obj.title = "%s(%s%03d)" % (name, self.PREFIX, row+1)
if suffix is not None:
self.obj.title += " "+suffix(param)
title = str("%s(%s)" % (name, suffix(param)))
else:
title = str("%s()" % name)
self.obj.copy_data_from(self.orig)
self.objs.append(self.obj)
if len(self.objs) == 1: self.objs = self.objs[0]
if addmap:
self.compute_11(name, lambda m, p: (self.objs, None), None, onein=onein)
#------Setup Key Event
def _key_end(self, filter, event):
#print "key stop event"
self.key_stop = True
def _delete(self, filter, event):
self.delete = True
self.func(self.objs, self.param, None, None)
self.delete = False
filter.plot.replot()
def setup_KeyEvent(self, parent, action):
baseplot, start_state = parent.start_state.items()[-1]
filter = baseplot.filter
if action == "Cursor":
self.delete = False
filter.add_event(start_state,
KeyEventMatch((Qt.Key_Space,)),
self._close_cursor, start_state)
filter.add_event(start_state,
KeyEventMatch((Qt.Key_Backspace, Qt.Key_Minus, Qt.Key_Delete)),
self._delete, start_state)
elif action == "SingleClick":
filter.add_event(start_state,
MouseEventMatch(QEvent.MouseButtonPress, Qt.LeftButton, Qt.NoModifier),
self._end_cursor, start_state)
elif action == "Stop":
self.key_stop = False
filter.removeEventFilter(filter)
filter.add_event(start_state,
KeyEventMatch((Qt.Key_Space,)),
self._key_end, start_state)
#------Data Processing
class ScriptParameter:
def __init__(self, title, params):
self._name = title
self._items = params
self.title = title
for p in params:
setattr(self, p, params[p])
def get_title(self):
return self.title
def edit(self, parent=None):
return True
def read_defaults(self, param):
if param == None: return param
filename = os.getenv("HOME") + "/.nod3/" + param.get_title().replace(" ","")
if osp.exists(filename):
f = open(filename, "r")
try:
pdict = cPickle.load(f)
for p in pdict:
setattr(param, p, pdict[p])
except:
pass
f.close()
return param
def write_defaults(self, param):
if param != None:
# do not write script parameters as next defaults
##if type(param._items) == dict: return
directory = os.getenv("HOME") + "/.nod3"
if not osp.exists(directory):
os.mkdir(directory)
filename = os.getenv("HOME") + "/.nod3/" + param.get_title().replace(" ","")
f = open(filename, "w")
pdict = {}
if type(param._items) == dict:
for i in param._items.keys():
pdict[i] = getattr(param, i)
else:
for i in param._items:
pdict[i._name] = getattr(param, i._name)
cPickle.dump(pdict, f)
f.close()
def getparams(self, m, key, value):
param = self.param
setattr(param, key, value)
if param is not None:
if not param.edit(parent=self.parent()):
return
htext = ""
delim = ":"
for i in param._items:
if hasattr(i, '_name'):
val = getattr(param, i._name)
if type(i) in (StringItem, ChoiceItem):
val = str("'%s'" % val)
htext += str("%s=%s, " % (i._name, val))
else:
val = getattr(param, i)
if type(val) == str:
val = str("'%s'" % val)
htext += str("%s=%s, " % (i, val))
htext = htext[:-2]
m.title += " "+htext
title = str("NOD3%s%s(%s)" % (delim, self.name, htext))
m.header.add_history(title)
return param
def apply_11_func(self, objs, func, param, onein):
newobjs = []
if not onein: objs = [objs]
for obj in objs:
x, param = func(obj, param)
# check for array (cursor)
if hasattr(x, 'shape'):
objs.data = x
else:
objs = x
if type(objs) != list: objs = [objs]
for obj in objs:
# setup metadata dictionary from header
if hasattr(obj, 'header'):
obj.header["DATAMAX"] = (np.nanmax(obj.data), "MAX VALUE OF ARRAY")
obj.header["DATAMIN"] = (np.nanmin(obj.data), "MIN VALUE OF ARRAY")
obj.metadata, obj.history = self.set_metadata(obj.header)
newobjs.append(obj)
return newobjs
def handle_input_output(self, objs, func, param, onein=True):
try:
newobjs = self.apply_11_func(objs, func, param, onein)
self.write_defaults(param)
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
finally:
self.emit(SIGNAL("status_message(QString)"), "")
QApplication.restoreOverrideCursor()
for obj in newobjs:
if self.display: self.add_object(obj)
else: self.replace_object(obj)
if hasattr(self, 'ids'):
self.ids.append(self.listwidget.selectionModel().currentIndex())
def compute_11(self, name, func, param=None, onein=True, extern=False, MType=False,
one_param_for_all=True, suffix=None, setpar=None):
# close source list box if open
if hasattr(self, 'LView'):
if hasattr(self, 'N'): del self.N
if self.LView.isVisible():
self.LView.close()
# close pyplot figure if open
if hasattr(self, 'fig'):
if hasattr(self, 'N'): del self.N
try:
if self.fig.win.isVisible():
self.fig.win.close()
del self.fig
except: pass
#self.APP_NAME = APP_NAME
self.APP_NAME = name
# scripting:
if not hasattr(param, '_name'):
param = self.read_defaults(param)
# change default from task:
if setpar != None:
setpar = setpar.split("=")
setattr(param, *setpar)
if extern:
self.param = cp.copy(param)
param = None
if param is not None and one_param_for_all:
if not param.edit(parent=self.parent()):
return
if param is None: htext=None
else:
htext = ""
for i in param._items:
if hasattr(i, '_name'):
val = getattr(param, i._name)
if type(i) in (StringItem, ChoiceItem):
val = _("'%s'") % val
htext += _("%s=%s, ") % (i._name, val)
else:
val = getattr(param, i)
if type(val) == str:
val = str("'%s'" % val)
htext += str("%s=%s, " % (i, val))
htext = htext[:-2]
rows = self._get_selected_rows()
if onein == 2: onein = False
in_objs = []
self.ids = []
for row in rows:
self.cmap = self.items[row].imageparam.colormap
self.row = row
if param is not None and not one_param_for_all:
if not param.edit(parent=self.parent()):
return
orig = self.objects[row]
obj = self.PARAMCLASS()
obj.copy_data_from(orig)
if onein:
obj.title = "%s(%s%03d)" % (name, self.PREFIX, row+1)
delim = ":"
else:
mtype = ""
if 'MAPTYPE' in obj.header: mtype += obj.header['MAPTYPE']
#if 'MAPTYPE' in obj.header: mtype += obj.header['MAPTYPE']
if 'RXHORN' in obj.header: mtype += str("-%d" % obj.header['RXHORN'])
#if 'RXHORN' in obj.header: mtype += str("-%d" % obj.header['RXHORN'])
# changed 2013/06/14 displays maps rather than maptype!
#if mtype != "":
if mtype == "":
#title = str("%s%s" % (self.PREFIX, mtype))
title = mtype
else:
if MType:
title = ", ".join(["%s" % (mtype.split("-")[0])])
else:
title = ", ".join(["%s%03d" % (self.PREFIX, row+1) for row in self._get_selected_rows()])
obj.title = name + "(%s)" % title
#delim = ">"
delim = ":"
#obj.copy_data_from(orig)
if htext is not None:
obj.title += " "+htext
title = str("NOD3%s%s(%s)" % (delim, name, htext))
#title = _("NOD3%s%s(%s)") % (delim, name, htext)
else:
title = str("NOD3%s%s()" % (delim, name))
# write new history entry
if not extern: obj.header.add_history(title)
self.repaint()
if onein:
self.emit(SIGNAL("status_message(QString)"),
_("Computing:")+" "+obj.title)
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
self.handle_input_output([obj], func, param, onein)
else:
in_objs.append(obj)
if rows != [] and not onein:
self.emit(SIGNAL("status_message(QString)"),
_("Computing:")+" "+obj.title)
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
self.handle_input_output(in_objs, func, param, onein)
# add output objects to row selection
for id in self.ids:
self.listwidget.selectionModel().select(id, self.listwidget.selectionModel().Select)
if hasattr(self, 'isPlotted'):
del self.isPlotted
def hide_polygon(self):
if not hasattr(self, 'plot'): return
if hasattr(self, 'hide_overlay') and not self.hide_overlay: return
items = self.plot.get_items()
for item in items:
itm = str(item).split()[0].split(".")[-1]
if itm == "PolygonMapItem":
if item.isVisible():
item.hide()
def del_polygon(self, Name=None):
if not hasattr(self, 'plot'): return
items = self.plot.get_items()
if str(items[-1]).find("ImageStats") > 0:
self.plot.del_items([items[-1]])
return
ditems = []
for item in items:
iname = item.title().text()
itm = str(item).split()[0].split(".")[-1]
if Name == None and itm == "PolygonMapItem":
ditems.append(item)
elif iname == Name:
self.plot.del_items([item])
if ditems != []:
self.plot.del_items(ditems)
def removeNANedges(self, obj):
rows, cols = obj.data.shape
r = []
for row in range(rows):
if False in np.isnan(obj.data[row]): r.append(row)
c = []
for col in range(cols):
if False in np.isnan(obj.data[:,col]): c.append(col)
if r == [] or c == []:
return obj
j1 = r[0]
j2 = r[-1]+1
i1 = c[0]
i2 = c[-1]+1
obj.header['CRPIX1'] -= i1
obj.header['CRPIX2'] -= j1
obj.data = obj.data[j1:j2,i1:i2]
if hasattr(obj, 'sidmap'): obj.sidmap = obj.sidmap[j1:j2,i1:i2]
if hasattr(obj, 'parmap'): obj.parmap = obj.parmap[j1:j2,i1:i2]
newrows, newcols = obj.data.shape
obj.header['NAXIS1'] = newcols
obj.header['NAXIS2'] = newrows
return obj
class ImageFT(ObjectFT):
PARAMCLASS = ImageParam
PREFIX = "map"
#------ObjectFT API
def setup(self, toolbar):
ObjectFT.setup(self, toolbar)
self.display = True
# File actions
open_action = create_action(self, _("Open image..."),
icon=get_icon('fileopen.png'),
tip=_("Open an image"),
triggered=self.open_image)
script_action = create_action(self, _("Open script..."),
icon=get_icon('edit.png'),
tip=_("Open a script"),
triggered=self.open_script)
save_action = create_action(self, _("Save image..."),
icon=get_icon('filesave.png'),
tip=_("Save selected FITS map(s)"),
triggered=self.save_image)
nod3save_action = create_action(self, _("Save NOD3 image..."),
icon=get_icon('filesave.png'),
tip=_("Save selected NOD3-FITS map(s)"),
triggered=self.save_NOD3image)
self.actlist_1more += [save_action, nod3save_action]
self.file_actions = [open_action, script_action, save_action, nod3save_action]
# Operation actions
rotate_menu = QMenu(_("Rotation"), self)
hflip_action = create_action(self, _("Flip horizontally"),
triggered=self.HFlip)
vflip_action = create_action(self, _("Flip vertically"),
triggered=self.VFlip)
rot90_action = create_action(self, _("Rotate 90° right"),
triggered=self.Rotate270)
rot270_action = create_action(self, _("Rotate 90° left"),
triggered=self.Rotate90)
rotate_action = create_action(self, _("Rotate arbitrarily..."),
triggered=self.Rotate)
resize_action = create_action(self, _("Resize"),
triggered=self.Resize)
roi_action = create_action(self, _("ROI extraction"),
triggered=self.ROI)
swapaxes_action = create_action(self, _("Swap X/Y axes"),
triggered=self.SwapAxes)
self.actlist_1 += [resize_action]
self.actlist_1more += [roi_action, swapaxes_action,
hflip_action, vflip_action,
rot90_action, rot270_action, rotate_action]
add_actions(rotate_menu, [hflip_action, vflip_action,
rot90_action, rot270_action, rotate_action])
self.operation_actions += [None, rotate_menu, None,
resize_action, roi_action, swapaxes_action]
# NOD3 actions
self.NOD3_all_actions()
add_actions(toolbar, [open_action, script_action, save_action])
def NOD3_all_actions(self):
self.cwd = os.getcwd() + "/"
if sys.path[0] == "": sys.path.pop(0)
self.Nod3AppList = {}
for toolb in NOD3_toolbar:
if toolb == "User":
toolpath = os.getenv("HOME") + "/Nod3Apps"
else:
toolpath = sys.path[0] + "/" + toolb
sys.path.insert(2, toolpath)
tasklist = []
if osp.exists(toolpath):
all_tasks = os.listdir(toolpath)
all_tasks.sort()
tasklist = []
for task in all_tasks:
if task[-3:] == ".py":
taskname = task[:-3]
exec "import " + taskname
title = eval(taskname + ".title")
tip = eval(taskname + ".tip")
try: onein = eval(taskname + ".onein")
except AttributeError: onein = True
setattr(self, taskname, eval(taskname+".NOD3_App(self)"))
xtask = create_action(self, _(title),
tip = _(tip),
#checkable=True,
#enabled=True,
triggered = eval("self."+taskname+".compute_app"))
xtask.setStatusTip(tip)
#xtask.statusTip()
xtask.toolTip = tip
if onein == 2: self.actlist_2 += [xtask]
elif onein == -1: self.actlist_1 += [xtask]
elif onein: self.actlist_1more += [xtask]
else: self.actlist_2more += [xtask]
tasklist.append(xtask)
self.Nod3AppList[title.replace(" ", "")] = "self."+taskname+".compute_app"
#self.actlist_1more += tasklist
setattr(self, toolb + "_actions", tasklist)
def hist_range_threshold(self, hist, bin_edges, percent):
hist = np.concatenate((hist, [0]))
threshold = .5*percent/100*hist.sum()
i_bin_min = np.cumsum(hist).searchsorted(threshold)
i_bin_max = -1-np.cumsum(np.flipud(hist)).searchsorted(threshold)
return bin_edges[i_bin_min], bin_edges[i_bin_max]
def lut_range_threshold(self, item, bins, percent):
hist, bin_edges = self.color_get_histogram(item, bins)
return self.hist_range_threshold(hist, bin_edges, percent)
def color_get_histogram(self, item, nbins):
"""interface de IHistDataSource"""
from guiqwt._scaler import _histogram
if item.data is None:
return [0,], [0,1]
_min = np.nanmin(item.data)
_max = np.nanmax(item.data)
if item.data.dtype in (np.float64, np.float32):
bins = np.unique(np.array(np.linspace(_min, _max, nbins+1),
dtype=item.data.dtype))
else:
bins = np.arange(_min, _max+2, dtype=item.data.dtype)
res2 = np.zeros((bins.size+1,), np.uint32)
_histogram(item.data.flatten(), bins, res2)
res = res2[1:-1], bins
return res
def make_item(self, row):
image = self.objects[row]
class DirParam(DataSet):
cmap = StringItem("ColorMap:", default='gray')
param = DirParam("cmap", "Setup of last choosen color map")
if hasattr(self, 'cmap'):
cmap = self.cmap
param.cmap = cmap
#elif hasattr(self, 'last_item'):
# cmap = self.last_item.get_color_map_name()
# param.cmap = cmap
# self.cmap = cmap
else:
param = self.read_defaults(param)
if param != None: cmap = param.cmap
self.cmap = cmap
self.write_defaults(param)
##print 'cmap in make_item', cmap
data = cp.copy(image.data.real)
#item = make.image(image.data.real, title=image.title, colormap=cmap, \
try:
item = make.image(image.data.real, title="", colormap=cmap, \
interpolation='nearest',
xformat='%.3f', yformat='%.3f', zformat='%.3f',
alpha = self.Alpha, alpha_mask=self.AlphaMask,
eliminate_outliers=self.Outliers)
#eliminate_outliers=None)
except:
item = make.image(image.data.real, title="",
interpolation='nearest',
xformat='%.3f', yformat='%.3f', zformat='%.3f',
alpha = self.Alpha, alpha_mask=self.AlphaMask,
eliminate_outliers=self.Outliers)
if self.Take:
lut_range = [self.Lower, self.Upper]
else:
lut_range = self.lut_range_threshold(item, 256, self.Outliers)
self.item = item
# hide border_rect patch self.select
item.select = self.select
# new get_stats patch self.get_stats
item.get_stats = self.get_stats
item.set_interpolation(self.InterpolationMode, self.IntSize)
item.set_data(image.data.real, lut_range=lut_range)
item.header = image.header
self.items[row] = item
self.last_item = item
if 'CDELT1' in item.header:
if item.header['CDELT1'] < 0:
self.item.LABEL_ANCHOR = "BR"
else:
self.item.LABEL_ANCHOR = "BL"
return item
def get_closest_index_rect(self, x0, y0, x1, y1):
px0, py0 = self.items[self.row].get_pixel_coordinates(x0, y0)
px1, py1 = self.items[self.row].get_pixel_coordinates(x1, y1)
i0 = min(nint(px0), nint(px1))
i1 = max(nint(px0), nint(px1))
j0 = min(nint(py0), nint(py1))
j1 = max(nint(py0), nint(py1))
return i0, j0, i1, j1
def get_stats(self, xx0, yy0, xx1, yy1):
"""Return formatted string with stats on image rectangular area
(output should be compatible with AnnotatedShape.get_infos)"""
ix0, iy0, ix1, iy1 = self.get_closest_index_rect(xx0, yy0, xx1, yy1)
#ix0, iy0, ix1, iy1 = self.items[self.row].get_closest_index_rect(xx0, yy0, xx1, yy1)
data = np.array(self.items[self.row].data[iy0:iy1, ix0:ix1])
x0 = min(xx0,xx1)
x1 = max(xx0,xx1)
y0 = min(yy0,yy1)
y1 = max(yy0,yy1)
rows, cols = data.shape
mask = ~np.isnan(data)
xfmt = self.item.imageparam.xformat
yfmt = self.item.imageparam.yformat
zfmt = self.item.imageparam.zformat
if len(data[mask]) > 0:
mean = data[mask].mean()
std = data[mask].std()
zmin = np.nanmin(data)
zmax = np.nanmax(data)
else:
mean = np.nan
std = np.nan
zmin = np.nan
zmax = np.nan
if self.AxesUseTime:
if self.AxisUseHour:
tx0 = TimeDelta(x0/15.0,'h')
tx1 = TimeDelta(x1/15.0,'h')
else:
tx0 = TimeDelta(x0,'d')
tx1 = TimeDelta(x1,'d')
ty0 = TimeDelta(y0,'d')
ty1 = TimeDelta(y1,'d')
return "<br>".join([
u"Box:%dx%d" % (cols, rows),
u"<b>σ(z) = " + zfmt % std + "</b>",
u"‹z› = " + zfmt % mean,
u"z_min = " + zfmt % zmin,
u"z_max = " + zfmt % zmax,
])
else:
return "<br>".join([
u"Box:%dx%d" % (cols, rows),
u"<b>σ(z) = " + zfmt % std + "</b>",
u"‹z› = " + zfmt % mean,
u"z_min = " + zfmt % zmin,
u"z_max = " + zfmt % zmax,
])
def update_item(self, row):
image = self.objects[row]
item = self.items[row]
#lut_range = [item.min, item.max]
if not self.Separate:
if self.Take:
lut_range = [self.Lower, self.Upper]
else:
#lut_range = [np.nanmin(item.data), np.nanmax(item.data)]
lut_range = self.lut_range_threshold(item, 256, self.Outliers)
item.set_data(image.data.real, lut_range=lut_range)
item.set_interpolation(self.InterpolationMode, self.IntSize)
item.imageparam.label = "" #image.title
if hasattr(self, 'xformat'):
item.imageparam.xformat = self.xformat
item.imageparam.yformat = self.yformat
item.imageparam.zformat = self.zformat
try:
item.plot().update_colormap_axis(item)
except: pass
##print self.cmap, 'update', row, self.items[row].imageparam.colormap
#------Image operations
def Rotate(self):
boundaries = ('constant', 'nearest', 'reflect', 'wrap')
prop = ValueProp(False)
class RotateParam(DataSet):
angle = FloatItem(u"%s (°)" % _(u"Angle"))
mode = ChoiceItem(_(u"Mode"), zip(boundaries, boundaries),
default=boundaries[0])
#cval = FloatItem(_("cval"), default=-1.0,
# help=_(u"Value used for points outside the "
# u"boundaries of the input if mode is "
# u"'constant'"))
reshape = BoolItem(_(u"Reshape the output array"), default=True,
help=_(u"Reshape the output array "
u"so that the input array is "
u"contained completely in the output"))
prefilter = BoolItem(_(u"Prefilter the input image"),
default=True).set_prop("display", store=prop)
order = IntItem(_(u"Order"), default=3, min=0, max=5,
help=_("Spline interpolation order")
).set_prop("display", active=prop)
param = RotateParam(_("Rotation"))
def function(m, p):
if not 'CRPIX1' in m.header:
m.data = map_rotate(m.data, p)
m = self.removeNANedges(m)
return m,p
rows1, cols1 = m.data.shape
m.data = map_rotate(m.data, p)
m = self.removeNANedges(m)
if p.reshape:
RAD = np.pi/180
rows, cols = m.data.shape
xpix1 = m.header['CRPIX1'] - cols1/2
ypix1 = m.header['CRPIX2'] - rows1/2
sina = np.sin(RAD*p.angle)
cosa = np.cos(RAD*p.angle)
xpix, ypix = np.dot([xpix1, ypix1], [[cosa, -sina], [sina, cosa]])
m.header['CRPIX1'] = cols/2 + xpix
m.header['CRPIX2'] = rows/2 + ypix
return m, p
#import scipy.ndimage as spi
from nodmath import map_rotate
self.compute_11("Rotate", lambda m, p: function(m, p), param)
def Rotate90(self):
def function(m, p):
m.data = np.rot90(m.data)
helem = ['NAXIS', 'CTYPE', 'CRVAL', 'CRPIX', 'CDELT', 'CROTA']
for h in helem:
if h+'1' in m.header and h+'2' in m.header:
#if h+'1' in m.header and h+'2' in m.header:
n1 = m.header[h+'1']
n2 = m.header[h+'2']
m.header[h+'1'] = n2
m.header[h+'2'] = n1
return m, p
self.compute_11("Rotate90", lambda m, p: function(m, p))
def Rotate270(self):
def function(m, p):
m.data = np.rot90(m.data, 3)
helem = ['NAXIS', 'CTYPE', 'CRVAL', 'CRPIX', 'CDELT', 'CROTA']
for h in helem:
if h+'1' in m.header and h+'2' in m.header:
#if h+'1' in m.header and h+'2' in m.header:
n1 = m.header[h+'1']
n2 = m.header[h+'2']
m.header[h+'1'] = n2
m.header[h+'2'] = n1
#m.header['CDELT1'] *= -1
#m.header['CDELT2'] *= -1
return m, p
self.compute_11("Rotate270", lambda m, p: function(m, p))
def HFlip(self):
def function(m, p):
m.data = np.fliplr(m.data)
#m.header['CDELT1'] *= -1
return m, p
self.compute_11("HFlip", lambda m, p: function(m, p))
def VFlip(self):
def function(m, p):
m.data = np.flipud(m.data)
#m.header['CDELT2'] *= -1
return m, p
self.compute_11("VFlip", lambda m, p: function(m, p))
def Resize(self):
rows = self._get_selected_rows()
obj = self.objects[rows[0]]
original_size = obj.data.shape[1], obj.data.shape[0]
from guiqwt.resizedialog import ResizeDialog
dlg = ResizeDialog(self.plot, new_size=original_size,
old_size=original_size,
text=_("Destination size:"))
if not dlg.exec_():
return
boundaries = ('constant', 'nearest', 'reflect', 'wrap')
prop = ValueProp(False)
class ResizeParam(DataSet):
#zoom = FloatItem(_(u"Zoom"), default=dlg.get_zoom())
mode = ChoiceItem(_(u"Mode"), zip(boundaries, boundaries),
default=boundaries[0])
cval = FloatItem(_("cval"), default=-1.0,
help=_(u"Value used for points outside the "
u"boundaries of the input if mode is "
u"'constant'"))
prefilter = BoolItem(_(u"Prefilter the input image"),
default=True).set_prop("display", store=prop)
order = IntItem(_(u"Order"), default=4, min=0, max=5,
help=_("Spline interpolation order")
).set_prop("display", active=prop)
param = ResizeParam(_("Resize"))
import scipy.ndimage as spi
def function(m, p):
if not hasattr(p, 'zoom'):
p.zoom = dlg.get_zoom()
if p.cval < 0.0: p.cval = np.nan
m.data = spi.interpolation.zoom(m.data, p.zoom, order=p.order,
mode=p.mode, cval=p.cval,
prefilter=p.prefilter)
m.header['NAXIS2'], m.header['NAXIS1'] = m.data.shape
m.header['CRPIX1'] *= p.zoom
m.header['CRPIX2'] *= p.zoom
m.header['CDELT1'] /= p.zoom
m.header['CDELT2'] /= p.zoom
return m, p
self.compute_11("Resize", lambda m, p: function(m, p),
param, suffix=lambda p: u"zoom=%.3f" % p.zoom)
def ROI(self):
class ROIParam(DataSet):
row1 = IntItem(_("First row index"), default=0, min=-1)
row2 = IntItem(_("Last row index"), default=-1, min=-1)
col1 = IntItem(_("First column index"), default=0, min=-1)
col2 = IntItem(_("Last column index"), default=-1, min=-1)
param = ROIParam(_("ROI extraction"))
def function(m, p):
m.data = m.data.copy()[p.row1:p.row2, p.col1:p.col2]
return m, p
self.compute_11("ROI", lambda m, p: function(m, p),
param, suffix=lambda p: u"rows=%d:%d,cols=%d:%d"
% (p.row1, p.row2, p.col1, p.col2))
def SwapAxes(self):
def function(m, p):
m.data = m.data.T
helem = ['NAXIS', 'CTYPE', 'CRVAL', 'CRPIX', 'CDELT', 'CROTA']
for h in helem:
if h+'1' in m.header and h+'2' in m.header:
n1 = m.header[h+'1']
n2 = m.header[h+'2']
m.header[h+'1'] = n2
m.header[h+'2'] = n1
m.header['CDELT2'] *= -1
return m, p
self.compute_11("SwapAxes", lambda m, p: function(m, p))
def set_metadata(self, header):
metadata = {}
if header != None:
try:
for key in header.keys():
if key != "HISTORY" and key != "COMMENT" and key != "":
try:
value = header[key]
metadata[key] = value
except:
pass
except:
for item in header.items():
if len(item) == 2:
key = item[0]
if key != "HISTORY" and key != "COMMENT" and key != "":
value = item[1]
metadata[key] = value
history = {}
n = 0
hist = []
append = False
if 'HISTORY' in header:
for h in header['HISTORY']:
h = str(h)
#if h.find("NOD3:") >=0 or h.find("NOD3>") >=0:
if "NOD3:" or "NOD3>" in h:
hist.append(h)
if h.strip()[-1] == ")":
append = False
else:
append = True
elif append:
hist[-1] += h
for h in hist:
h = str(h)
if h.find("NOD3:") >=0 or h.find("NOD3>") >=0:
n += 1
if h.find(":") > 0:
history[str("%4.4d" % n)] = h.split("NOD3:")[1]
elif h.find(">") > 0:
history[str("%4.4d" % n)] = h.split("NOD3:")[1]
return metadata, history
def save_script(self, hlines):
"""Save script file"""
from nod3scripting import exec_script_save_dialog
class DirParam(DataSet):
MyNOD3SCR = StringItem("MyNOD3SCR:", default=NOD3DIR)
param = DirParam("MyNOD3SCR", "Setup the NOD3 Script directory name")
param = self.read_defaults(param)
if param != None: MyNOD3SCR = param.MyNOD3SCR
scriptname = exec_script_save_dialog(self, hlines, outdir=MyNOD3SCR, app_name=APP_NAME)
if scriptname:
os.chdir(osp.dirname(scriptname))
param.MyNOD3SCR = osp.dirname(scriptname)
self.write_defaults(param)
def check_app_input(self, app):
for each in self.actlist_2more:
if each.text() == app:
return self._get_selected_rows()
#return 3
for each in self.actlist_2:
if each.text() == app:
return 2
return 1
def open_script(self):
"""Open script file"""
from nod3scripting import exec_script_open_dialog
class DirParam(DataSet):
NOD3SCR = StringItem("NOD3SCR:", default=NOD3DIR)
param = DirParam("NOD3SCR", "Setup the NOD3 Script directory name")
param = self.read_defaults(param)
if param != None: NOD3SCR = param.NOD3SCR
self.selrows = self.listwidget.selectionModel().selectedRows()
rows = self._get_selected_rows()
if rows == []: return
for scriptname in exec_script_open_dialog(self, basedir=NOD3SCR, app_name=APP_NAME):
param.NOD3SCR = osp.dirname(scriptname)
fin = open(scriptname, "r")
apps = fin.readlines()
fin.close()
first = True
for app in apps:
if app.strip() != "" and app.strip()[0] != "#":
app = app.replace("\n", "")
try:
appname, apparam = app.split("(")
apparam = "(" + apparam
except ValueError:
appname = app
apparam = "()"
nselect = self.check_app_input(appname)
#if first:
# if nselect < len(rows):
# msg = str("too many rows selected\nonly %d row(s) allowed" % nselect)
# QMessageBox.critical(self.parent(), APP_NAME,
# _(u"Error:")+"\n%s" % msg)
# break
first = False
if appname in self.Nod3AppList:
apptask = self.Nod3AppList[appname]
apparam = apparam[:apparam.find(")")+1]
try:
eval(apptask+apparam)
#self.display = False
except Exception, msg:
import traceback
traceback.print_exc()
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % msg)
break
elif hasattr(self, appname):
apparam = apparam[:apparam.find(")")+1]
eval("self."+appname+apparam)
else:
msg = str("no such application: %s" % app)
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
break
#self.refresh_list(new_current_row='last')
self.write_defaults(param)
def open_image(self, infile=None):
"""Open image file"""
from nod3fits import exec_fits_open_dialog
class DirParam(DataSet):
NOD3DIR = StringItem("NOD3DIR:", default=NOD3DIR)
param = DirParam("NOD3DIR", "Setup the NOD3FITS directory name")
param = self.read_defaults(param)
if param != None: NOD3DIR = param.NOD3DIR
for filename, metadata, data, s, p in exec_fits_open_dialog(self, basedir=NOD3DIR,
app_name=APP_NAME, mapnum=0, infile=infile ):
if type(data) == type(None) or type(metadata) == type(None):
msg = "Data not in NOD3 FITS format"
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
return
param.NOD3DIR = osp.dirname(filename)
try: os.chdir(osp.dirname(filename))
except: pass
fname = os.path.split(filename)[-1]
self.fname = fname
if type(metadata) != type(None):
if 'EXTNAME' in metadata: extname = metadata['EXTNAME']
#if 'EXTNAME' in metadata: extname = metadata['EXTNAME']
else: extname = "MAP-I"
extname = extname.replace("MAP-", "")
if 'RXHORN' in metadata: horn = metadata['RXHORN']
#if 'RXHORN' in metadata: horn = metadata['RXHORN']
else: horn = 0
image = ImageParam()
#image.title = filename
#image.title = str("%s(%s,h=%i)" % (fname, extname, horn))
image.title = str("%s(%s)" % (fname, extname))
image.data = data
image.header = metadata
image.header["FILENAME"] = (fname, 'File name')
# setup sidereal time and parallactic angle
if type(s) != type(None):
image.sidmap = s
if type(p) != type(None):
image.parmap = p
# setup metadata dictionary from header
image.metadata, image.history = self.set_metadata(metadata)
if type(data) != type(None):
self.add_object(image)
else:
msg = "Data not in NOD3 FITS format"
QMessageBox.critical(self.parent(), APP_NAME,
_(u"Error:")+"\n%s" % str(msg))
self.write_defaults(param)
def save_NOD3image(self, dim=2):
self.save_image(nod3=True)
#def save_image(self):
def save_image(self, dim=2, nod3=False):
"""Save selected image"""
from nod3fits import exec_fits_save_dialog
class DirParam(DataSet):
NOD3OUT = StringItem("NOD3OUT:", default=NOD3DIR)
if nod3:
self.SidOut = True
self.ParOut = True
param = DirParam("NOD3OUT", "Setup the NOD3FITS directory name")
param = self.read_defaults(param)
if param != None: NOD3OUT = param.NOD3OUT
rows = self._get_selected_rows()
self.VERSION = VERSION
from guiqwt.qthelpers import exec_image_save_dialog
if not dim: dim = 2
filename = exec_fits_save_dialog(self, rows, outdir=NOD3OUT,
#app_name=APP_NAME)
app_name=APP_NAME, dim=dim, nod3=nod3)
if filename:
os.chdir(osp.dirname(filename))
param.NOD3OUT = osp.dirname(filename)
self.write_defaults(param)
def old_save_image(self):
"""Save selected image"""
from nod3fits import exec_fits_save_dialog
class DirParam(DataSet):
NOD3OUT = StringItem("NOD3OUT:", default=NOD3DIR)
param = DirParam("NOD3OUT", "Setup the NOD3FITS directory name")
param = self.read_defaults(param)
if param != None: NOD3OUT = param.NOD3OUT
rows = self._get_selected_rows()
for row in rows:
obj = self.objects[row]
# update new fits metadata from properties menu
update_fits_metadata(obj)
obj.header['NOD3VERS'] = (VERSION, 'NOD3 software version')
from guiqwt.qthelpers import exec_image_save_dialog
filename = exec_fits_save_dialog(obj.data, obj.header, self, outdir=NOD3OUT,
app_name=APP_NAME, dim=dim)
if filename:
os.chdir(osp.dirname(filename))
param.NOD3OUT = osp.dirname(filename)
self.write_defaults(param)
def nan_check(self, data, val, weight=False):
Data = data.copy()
mask = np.isfinite(Data)
Data[~mask] = val
if weight:
return Data, np.array(mask, dtype=float)
else:
return Data
class DockablePlotWidget(DockableWidget):
LOCATION = Qt.RightDockWidgetArea
def __init__(self, parent, plotwidgetclass, toolbar):
super(DockablePlotWidget, self).__init__(parent)
self.toolbar = toolbar
layout = QVBoxLayout()
self.plotwidget = plotwidgetclass()
layout.addWidget(self.plotwidget)
self.setLayout(layout)
self.setup()
def get_plot(self):
return self.plotwidget.plot
def setup(self):
title = unicode(self.toolbar.windowTitle())
self.plotwidget.add_toolbar(self.toolbar, title)
if isinstance(self.plotwidget, ImageWidget):
self.plotwidget.register_all_image_tools()
else:
self.plotwidget.register_all_curve_tools()
#------DockableWidget API
def visibility_changed(self, enable):
"""DockWidget visibility has changed"""
DockableWidget.visibility_changed(self, enable)
self.toolbar.setVisible(enable)
class DockableTabWidget(QTabWidget, DockableWidgetMixin):
LOCATION = Qt.LeftDockWidgetArea
def __init__(self, parent):
QTabWidget.__init__(self, parent)
DockableWidgetMixin.__init__(self, parent)
try:
from spyderlib.widgets.internalshell import InternalShell
class DockableConsole(InternalShell, DockableWidgetMixin):
LOCATION = Qt.BottomDockWidgetArea
def __init__(self, parent, namespace, message, commands=[]):
InternalShell.__init__(self, parent=parent, namespace=namespace,
message=message, commands=commands,
multithreaded=True)
DockableWidgetMixin.__init__(self, parent)
self.setup()
def setup(self):
font = QFont("Courier new")
font.setPointSize(10)
self.set_font(font)
self.set_codecompletion_auto(True)
self.set_calltips(True)
self.setup_calltips(size=600, font=font)
self.setup_completion(size=(300, 180), font=font)
except ImportError:
DockableConsole = None
class NOD3Proxy(object):
def __init__(self, win):
self.win = win
self.obj = self.win.mainwidget.imageft.objects
class CentralWidget(QSplitter):
def __init__(self, parent, toolbar, status):
QSplitter.__init__(self, parent)
self.setContentsMargins(10, 10, 10, 10)
self.setOrientation(Qt.Horizontal)
#self.imagewidget = ImageWidget(self, colormap=None, otherOptionsAvailable)
self.imagewidget = ImageWidget(self)
self.imagewidget.autoscale_mode = False
self.imageft = ImageFT(self, self.imagewidget.get_plot())
self.imageft.setup(toolbar)
self.connect(self.imageft, SIG_LUT_CHANGED, self.lut_range_changed)
self.item = None # image item
# add statusBar to show progress in NOD3 tools
self.msg = status.showMessage
self.imagewidget.Progress = status
self.imagewidget.Progress.showMessage = self.showMessage
self.imagewidget.add_toolbar(toolbar, "default")
self.register_tools(toolbar)
#self.imagewidget.register_all_image_tools()
self.addWidget(self.imagewidget)
self.images = [] # List of ImageParam instances
self.lut_ranges = [] # List of LUT ranges
self.setStretchFactor(0, 0)
def showMessage(self, text, msecs=0):
self.msg(text, msecs=0)
qApp.processEvents()
def signal_handler(self, signum, frame):
self.STOP = True
def keyPressEvent(self, event):
qApp.processEvents()
self.KEY = event.key()
#print self.KEY, '1'
if self.KEY == Qt.Key_C and (event.modifiers() & Qt.ControlModifier):
self.imageft.STOP = True
elif self.KEY == Qt.Key_Escape:
self.imageft.STOP = True
def nod3_colormaps(self):
try:
import nod3luts
except:
return
cmlist = []
for name in dir(nod3luts):
if name.endswith("_data"):
obj = getattr(nod3luts, name)
if isinstance(obj, dict):
cmlist.append(name[1:-5])
for cmap_name in cmlist:
cmap = QwtLinearColorMap()
cmdata = getattr(nod3luts, "_"+cmap_name+"_data")
cm._setup_colormap(cmap, cmdata)
cm.register_extra_colormap(cmap_name, cmap)
self.cmlist = cmlist
def printer_command(self, plot, checked):
"""Activate tool"""
class PrintFilter(QwtPlotPrintFilter):
def __init__(self):
QwtPlotPrintFilter.__init__(self)
def color(self, c, item):
if not (self.options() & QwtPlotPrintFilter.CanvasBackground):
if item == QwtPlotPrintFilter.MajorGrid:
return Qt.darkGray
elif item == QwtPlotPrintFilter.MinorGrid:
return Qt.gray
if item == QwtPlotPrintFilter.Title:
return Qt.black
elif item == QwtPlotPrintFilter.AxisScale:
return Qt.black
elif item == QwtPlotPrintFilter.AxisTitle:
return Qt.black
return c
def font(self, f, _):
result = QFont(f)
result.setPointSize(int(f.pointSize()*1.25))
return result
printer = QPrinter(QPrinter.ScreenResolution)
#printer = QPrinter(QPrinter.HighResolution)
printer.PageSize(printer.A4)
printer.setFullPage(False)
printer.setDoubleSidedPrinting(False)
printer.setCreator('NOD3')
self.aspect = 1
for item in plot.items:
if item.isVisible():
if hasattr(item, 'data'):
rows, cols = item.data.shape
self.aspect = float(cols)/float(rows)
paperPixels = printer.pageRect(QPrinter.DevicePixel)
paperPixels = paperPixels.getRect() #get tuple of the "pixels on the paper"
paperWidth = paperPixels[2]
paperHeight = paperPixels[3]
margin = 32
off = abs(paperWidth-paperHeight)/4 + margin/2
if self.aspect < 1:
printer.setOrientation(printer.Portrait)
printer.setPageMargins(margin, margin+off, margin, margin+off, printer.Point)
else:
printer.setOrientation(printer.Landscape)
printer.setPageMargins(margin+off, margin, margin+off, margin, printer.Point)
printer.setColorMode(printer.Color)
#printer.setOutputFormat(QPrinter.PdfFormat) # test only
#try: plot.setCanvasBackground = Qt.black
#except: pass
dialog = QPrintDialog(printer, plot)
saved_in, saved_out, saved_err = sys.stdin, sys.stdout, sys.stderr
sys.stdout = None
diag = dialog.exec_()
sys.stdin, sys.stdout, sys.stderr = saved_in, saved_out, saved_err
if diag:
filter = PrintFilter()
if (QPrinter.GrayScale == printer.colorMode()):
filter.setOptions(QwtPlotPrintFilter.PrintAll
& ~QwtPlotPrintFilter.PrintBackground
| QwtPlotPrintFilter.PrintFrameWithScales)
#plot.set_aspect_ratio(ratio=np.sqrt(2.0), lock=True)
self.print_(plot, printer, filter)
def print_(self, plot, device, filter):
from nodmath import extract
for i in range(len(plot.items)):
if plot.items[i].isVisible():
break
self.data = 1*plot.items[i].data
rows, cols = self.data.shape
r = int(max(rows, cols)/20.0)
c = int(max(rows, cols)/14.0)
data = extract(self.data, shape=(rows+r, cols+c), position=((rows+r)/2, (cols-c)/2))
plot.items[i].data = data
plot.print_(device, filter)
plot.items[i].data = self.data
#plot.replot()
def save_widget(self, fname):
"""Grab widget's window and save it to filename (*.png, *.pdf)"""
fname = unicode(fname)
if hasattr(self.Plot.window(), 'frame'):
#palette = self.Plot.window().frame.palette()
#role = self.Plot.window().frame.backgroundRole()
#palette.setColor(role, QColor('white'))
#self.Plot.window().frame.setPalette(palette)
#self.Plot.window().frame.setFrameShadow(QFrame.Plain)
self.Plot.window().setStyleSheet("background-color: rgb(255,255,255); border:0px solid rgb(0, 0, 0)")
if fname.lower().endswith('.ps'):
printer = QPrinter()
printer.setOutputFormat(QPrinter.PostScriptFormat)
printer.setOrientation(QPrinter.Portrait)
#printer.setOrientation(QPrinter.Landscape)
printer.setPageMargins(2.5, 50.0, 10.0, 50.0, QPrinter.Millimeter)
printer.setOutputFileName(fname)
printer.setCreator('NOD3')
self.Plot.print_(printer)
elif fname.lower().endswith('.pdf'):
printer = QPrinter()
printer.setOutputFormat(QPrinter.PdfFormat)
printer.setOrientation(QPrinter.Portrait)
#printer.setOrientation(QPrinter.Landscape)
printer.setPageMargins(2.5, 50.0, 10.0, 50.0, QPrinter.Millimeter)
printer.setOutputFileName(fname)
printer.setCreator('NOD3')
self.Plot.print_(printer)
elif fname.lower().endswith('.png'):
#pixmap = QPixmap.grabWidget(self.Plot)
if hasattr(self.Plot.window(), 'frame'):
pixmap = QPixmap.grabWidget(self.Plot.window().frame)
else:
pixmap = QPixmap.grabWidget(self.Plot)
pixmap.save(fname, 'PNG')
elif fname.lower().endswith('.jpg'):
#pixmap = QPixmap.grabWidget(self.Plot)
if hasattr(self.Plot.window(), 'frame'):
pixmap = QPixmap.grabWidget(self.Plot.window().frame)
else:
pixmap = QPixmap.grabWidget(self.Plot)
pixmap.s1ave(fname, 'JPG')
elif fname.lower().endswith('.bmp'):
#pixmap = QPixmap.grabWidget(self.Plot)
if hasattr(self.Plot.window(), 'frame'):
pixmap = QPixmap.grabWidget(self.Plot.window().frame)
else:
pixmap = QPixmap.grabWidget(self.Plot)
pixmap.save(fname, 'BMP')
else:
raise RuntimeError(_("Unknown file extensions"))
self.Plot.window().setStyleSheet("")
def save_as_command(self, plot, checked):
"""Activate tool"""
#FIXME: Qt's PDF printer is unable to print plots including images
# --> until this bug is fixed internally, disabling PDF output format
# when plot has image items.
self.Plot = plot
#print dir(QPrinter)
formats = '%s (*.pdf)' % _('PDF document')
#formats += '\n%s (*.ps)' % _('PS document')
formats += '\n%s (*.bmp)' % _('BMP images')
formats += '\n%s (*.jpg)' % _('JPG images')
formats += '\n%s (*.png)' % _('PNG image')
#formats += '\n%s (*.pdf)' % _('PDF document')
#formats = '%s (*.png *.jpg)\n%s (*.pdf)' % (_('Images'), _('PDF document'))
formats = _add_all_supported_files(formats)
from guiqwt.interfaces import IImageItemType
for item in plot.get_items():
if IImageItemType in item.types():
break
fname, _f = getsavefilename(plot, _("Save as pixelmap"), _('pixelmap.png'), formats)
if fname:
#plot.get_active_item().border_rect.unselect()
background = str(plot.canvasBackground().name())
self.setStyleSheet("background-color: rgb(255,255,255); border:0px solid rgb(0, 0, 0)")
plot.setCanvasBackground(QColor(background))
self.save_widget(fname)
self.setStyleSheet("")
def register_tools(self, toolbar):
self.imagewidget.add_separator_tool()
self.imagewidget.register_standard_tools()
#self.imagewidget.add_separator_tool()
#self.register_nod3_tools(self.imagewidget)
# NOD3 defs
self.nod3_colormaps()
self.imagewidget.add_tool(ColormapTool)
self.imagewidget.add_tool(ContrastTool)
self.imagewidget.add_tool(CrossSectionTool)
#self.imagewidget.add_tool(ContrastPanelTool)
self.imagewidget.add_tool(ItemListPanelTool)
self.imagewidget.add_tool(ReverseYAxisTool)
self.imagewidget.add_tool(AspectRatioTool)
self.imagewidget.add_tool(ImageStatsTool)
self.imagewidget.add_tool(NOD3SegmentTool)
self.imagewidget.add_separator_tool()
#
SaveAsTool.activate_command = self.save_as_command
self.imagewidget.add_tool(SaveAsTool)
PrintTool.activate_command = self.printer_command
self.imagewidget.add_tool(PrintTool)
self.imagewidget.add_tool(NOD3HelpTool)
#self.imagewidget.add_tool(SnapshotTool)
#self.imagewidget.register_other_tools()
self.imagewidget.add_separator_tool()
self.imagewidget.get_default_tool().activate()
#
# more NOD3 tools
self.imagewidget.add_tool(TimeAxisTool)
self.default_cmaps = cm.get_colormap_list()
item_list = create_action(self, _("Item list..."),
icon=get_icon('item_list.png'),
tip=_("Item list manager"),
triggered=self.item_list)
clear_toggle = create_action(self, _("Clear overlays..."),
icon=get_icon('delete.png'),
tip=_("Clears display from all overlays and applications"),
triggered=self.imageft.clears_display)
grid_toggle = create_action(self, _("Grid toggle..."),
icon=get_icon('grid.png'),
tip=_("Toggles grid on and off"),
triggered=self.grid_toggle)
#add_actions(toolbar, [item_list, grid_toggle])
add_actions(toolbar, [item_list, clear_toggle])
def item_list(self):
if self.imagewidget.get_itemlist_panel().isVisible():
self.imagewidget.get_itemlist_panel().hide()
else:
self.imagewidget.get_itemlist_panel().show()
self.imagewidget.get_itemlist_panel().update()
def grid_toggle(self):
self.imagewidget.plot.grid.set_selectable(True)
if self.imagewidget.plot.grid.isVisible():
self.imagewidget.plot.grid.hide()
else:
self.imagewidget.plot.grid.show()
self.imagewidget.plot.replot()
#print self.imagewidget.get_itemlist_panel().isEnabled()
def lut_range_changed(self):
row = self.imagewidget.currentRow()
self.lut_ranges[row] = self.item.get_lut_range()
class MainWindow(QMainWindow):
def __init__(self, options):
QMainWindow.__init__(self)
if sys.path[0] == "": sys.path.pop(0)
self.setWindowIcon(get_icon(sys.path[0]+'/MPIfR.svg'))
self.setWindowTitle(APP_NAME)
# Welcome message in statusbar:
status = self.statusBar()
status.showMessage(_("Welcome to %s!") % APP_NAME, 5000)
toolbar = self.addToolBar(_("Data Processing Toolbar"))
self.mainwidget = CentralWidget(self, toolbar, status)
self.setCentralWidget(self.mainwidget)
self.connect(self.mainwidget, SIGNAL("status_message(QString)"),
status.showMessage)
# set InterpolationMode
if options.linear:
self.mainwidget.imageft.InterpolationMode = INTERP_LINEAR
else:
self.mainwidget.imageft.InterpolationMode = INTERP_NEAREST
# File menu
self.quit_action = create_action(self, _("Quit"), shortcut="Ctrl+Q",
icon=get_std_icon("DialogCloseButton"),
tip=_("Quit application"),
#triggered=self.close)
triggered=self.Quit)
self.file_menu = self.menuBar().addMenu(_("File"))
self.connect(self.file_menu, SIGNAL("aboutToShow()"),
self.update_file_menu)
# Edit menu
self.edit_menu = self.menuBar().addMenu(_("&Edit"))
self.connect(self.edit_menu, SIGNAL("aboutToShow()"),
self.update_edit_menu)
# Operation menu
self.operation_menu = self.menuBar().addMenu(_("Operations"))
self.connect(self.operation_menu, SIGNAL("aboutToShow()"),
self.update_operation_menu)
# NOD3 menu
self.nod3_actions = []
for tool in NOD3_toolbar:
setattr(self, tool+"_menu", self.menuBar().addMenu(_(tool)))
self.connect(eval("self."+tool+"_menu"), SIGNAL("aboutToShow()"),
lambda t=tool: self.update_nod3_menu(t))
self.nod3_actions.append(tool)
# View menu
self.view_menu = view_menu = self.createPopupMenu()
view_menu.setTitle(_(u"&View"))
self.menuBar().addMenu(view_menu)
self.connect(self.view_menu, SIGNAL("aboutToShow()"),
self.update_view_menu)
# Help menu
help_menu = self.menuBar().addMenu("?")
about_action = create_action(self, _("About..."),
icon=get_std_icon('MessageBoxInformation'),
triggered=self.about)
add_actions(help_menu, (about_action,))
# Eventually add an internal console (requires 'spyderlib')
self.nod3_proxy = NOD3Proxy(self)
if DockableConsole is None:
self.console = None
if options.console:
import time, scipy.signal as sps, scipy.ndimage as spi
import pyfits as pf
ns = {'nod3': self.nod3_proxy,
'np': np, 'sps': sps, 'spi': spi,
'os': os, 'sys': sys, 'osp': osp, 'time': time}
msg = "NOD3 single dish radio contiuum data reduction tools\n\n"\
"Modules imported at startup: "\
"os, sys, os.path as osp, time, "\
"numpy as np, scipy.signal as sps, scipy.ndimage as spi"\
"pyfits as pf"
self.console = DockableConsole(self, namespace=ns, message=msg)
self.console.setMinimumHeight(200)
self.add_dockwidget(self.console, _(u"Console"))
else:
self.console = None
# Show main window image plot panel
self.show()
# Input file defined
if options.filename:
self.filename = "./" + options.filename
self.mainwidget.imageft.open_image(infile=self.filename)
else:
self.filename = None
#------GUI refresh/setup
def Ask(self, msg):
ask = QMessageBox.question(self.parent(), 'NOD3', msg,
QMessageBox.Yes, QMessageBox.No)
if ask == QMessageBox.Yes: return True
else: return False
def Quit(self):
if self.Ask("Really want to quit without saveing images?"):
self.close()
def add_dockwidget(self, child, title):
"""Add QDockWidget and toggleViewAction"""
dockwidget, location = child.create_dockwidget(title)
self.addDockWidget(location, dockwidget)
return dockwidget
def update_file_menu(self):
self.file_menu.clear()
objectft = self.mainwidget.imageft
actions = objectft.file_actions+[None, self.quit_action]
add_actions(self.file_menu, actions)
def update_edit_menu(self):
self.edit_menu.clear()
objectft = self.mainwidget.imageft
add_actions(self.edit_menu, objectft.edit_actions)
def update_operation_menu(self):
self.operation_menu.clear()
objectft = self.mainwidget.imageft
add_actions(self.operation_menu, objectft.operation_actions)
def update_view_menu(self):
self.view_menu.clear()
objectft = self.mainwidget.imageft
add_actions(self.view_menu, objectft.view_actions)
# update NOD3 GUI menu
def update_nod3_menu(self, tool):
eval("self."+tool+"_menu.clear()")
objectft = self.mainwidget.imageft
add_actions(eval("self."+tool+"_menu"), eval("objectft."+tool+"_actions"))
#------?
def about(self):
from guiqwt import __version__ as qwtvers
from guidata import __version__ as datvers
from pyfits import __version__ as fitsvers
from numpy import __version__ as npvers
QMessageBox.about( self, _("About ")+APP_NAME,
"""<b>%s</b> v%s<br>%s<p>%s Peter Müller
<br>Copyright © 2012 MPIfR Bonn, Germany
<br>contact: peter@mpifr.de
<br>
<br>Based on guiqwt and guidata by Pierre Raybault
<br>Copyright © 2010 CEA
<p>Python %s, Numpy %s, Qt %s, PyQt %s %s %s
<br>GUIqwt %s, GUIdata %s, PyFits %s """ % \
(APP_NAME, VERSION, APP_DESC, _("Developed and maintained by"),
platform.python_version(), npvers,
QT_VERSION_STR, PYQT_VERSION_STR, _("on"), platform.system(),
qwtvers, datvers, fitsvers) )
def closeEvent(self, event):
rows = self.mainwidget.imageft._get_selected_rows()
if rows != []:
item = self.mainwidget.imageft.items[rows[-1]]
class DirParam(DataSet):
cmap = StringItem("ColorMap:", default='gray')
param = DirParam("cmap", "Setup of last choosen color map")
cmap = item.get_color_map_name()
if cmap in self.mainwidget.default_cmaps:
param.cmap = cmap
self.mainwidget.imageft.write_defaults(param)
if self.console is not None:
self.console.exit_interpreter()
if hasattr(self.mainwidget.imageft, 'LView'):
if self.mainwidget.imageft.LView.isVisible():
self.mainwidget.imageft.LView.close()
if hasattr(self.mainwidget.imageft, 'fig'):
try:
if self.mainwidget.imageft.fig.win.isVisible():
self.mainwidget.imageft.fig.win.close()
except: pass
event.accept()
def get_options():
"""
Convert options into commands
return commands, message
"""
import optparse
parser = optparse.OptionParser(usage="nod3.py [options]")
parser.add_option('-l', '--linear', dest="linear", action='store_true',
default=False,
help="Linear interpolation of display data")
parser.add_option('--session', dest="startup_session", default='',
help="Startup session")
parser.add_option('--defaults', dest="reset_to_defaults",
action='store_true', default=False,
help="Reset to configuration settings to defaults")
parser.add_option('--reset', dest="reset_session",
action='store_true', default=False,
help="Remove all configuration files!")
parser.add_option('--optimize', dest="optimize",
action='store_true', default=False,
help="Optimize Spyder bytecode (this may require "
"administrative privileges)")
parser.add_option('-w', '--workdir', dest="working_directory", default=None,
help="Default working directory")
parser.add_option('-d', '--debug', dest="debug", action='store_true',
default=False,
help="Debug mode (stds are not redirected)")
parser.add_option('--showconsole', dest="show_console",
action='store_true', default=False,
help="Show parent console (Windows only)")
parser.add_option('--multithread', dest="multithreaded",
action='store_true', default=False,
help="Internal console is executed in another thread "
"(separate from main application thread)")
parser.add_option('--profile', dest="profile", action='store_true',
default=False,
help="Profile mode (internal test, "
"not related with Python profiling)")
parser.add_option('-c', '--console', dest="console", action='store_true',
default=False,
help="Displays python console in an extra window")
parser.add_option('-f', '--file', dest="filename", default=False,
help="Default input file name")
options, _args = parser.parse_args()
return options
def main():
from guidata import qapplication
# **** Collect command line options ****
# Note regarding Options:
# It's important to collect options before monkey patching sys.exit,
# otherwise, optparse won't be able to exit if --help option is passed
options = get_options()
app = qapplication()
window = MainWindow(options)
if options.console: window.setGeometry(0,0,1200,940)
else: window.setGeometry(0,0,1200,760)
window.show()
app.exec_()
if __name__ == '__main__':
main()