Matrices added to docks, colormap added, option to choose range added

VERSION

@@ -1 +1 @@
-0.8.2
+0.8.3

src/VERSION

@@ -1 +1 @@
-0.8.2
+0.8.3

src/plugins/correlation_matrix.py

@@ -4,13 +4,13 @@
 import os
 import sys
 
-import pyqtgraph as pg
 from PyQt4.QtCore import *
 from PyQt4.QtGui import *
 
-from .util import file_io
 from .util import custom_qt_items as cqt
+from .util import file_io
 from .util.mygraphicsview import MyGraphicsView
+
 sys.path.append('..')
 import qtutil
 import pickle
@@ -23,13 +23,14 @@
 from .util.plugin import WidgetDefault
 from .util.plugin import PluginDefault
 from .util.custom_qt_items import RoiList
-from .util.custom_qt_items import RoiItemModel
 import functools
 import itertools
 import matplotlib.pyplot as plt
 import math
 from .util.custom_pyqtgraph_items import GradientLegend
 from .util.visualization_window import DockWindow
+from pyqtgraph.dockarea import *
+from .util import project_functions as pfs
 
 def calc_avg(roi, frames, image):
  mask = roi.getROIMask(frames, image, axes=(1, 2))
@@ -52,15 +53,87 @@ def selected_roi_changed(self, selection):
  self.widget.selected_rois_list.clear()
  self.widget.selected_rois_list.addItems([r for r in rois_selected])
 
+class DockWindowMat(DockWindow):
+ def __init__(self, win, parent, state=None, area=None, title=None):
+ super(DockWindowMat, self).__init__(None, area, title, parent)
+ self.parent = parent
+ self.state = state
+ self.connectivity_dialog = win
+ docks = range(len([i for i in self.area.docks.keys()]))
+ d = Dock("Connectivity Matrix", size=(500, 200), closable=True)
+ d.addWidget(win)
+ self.area.addDock(d, 'above', self.area.docks['d1'])
+
+ min_label = parent.min_sb.value()
+ max_label = parent.max_sb.value()
+ cm_type = parent.cm_comboBox.currentText()
+ view = MyGraphicsView(parent.project, parent=None, image_view_on=True)
+ l = GradientLegend(min_label, max_label, cm_type)
+ l.setParentItem(view.vb)
+ d = Dock("Gradient Legend", size=(500, 200), closable=True)
+ d.addWidget(view)
+ self.area.addDock(d, 'above', self.area.docks['d2'])
+
+ # close placeholder docks
+ for dock in docks:
+ self.area.docks['d'+str(dock+1)].close()
+ if state:
+ self.area.restoreState(self.state)
+
+ def setup_gradient_legend(self, l):
+ pass
+
+ def save_state(self):
+ save_loc = super().save_state()
+ with open(save_loc, 'rb') as input:
+ state = pickle.load(input)
+ try:
+ with open(save_loc, 'wb') as output:
+ pickle.dump([self.connectivity_dialog.model._data, self.connectivity_dialog.model.roinames,
+ state], output, -1)
+ except:
+ qtutil.critical(save_loc + " failed to save.")
+ return
+
+ def load_state(self):
+ filenames = QFileDialog.getOpenFileNames(
+ self, 'Load matrix', QSettings().value('last_vis_path'),
+ 'visualization window pickle (*.pkl)')
+ if not filenames:
+ return
+ QSettings().setValue('last_vis_path', os.path.dirname(filenames[0]))
+ for filename in filenames:
+ try:
+ with open(filename, 'rb') as input:
+ [mat_data, roinames, state] = pickle.load(input)
+ cm_type = self.parent.cm_comboBox.currentText()
+ win = ConnectivityDialog(self.parent, roinames, cm_type, mat_data)
+ new_dw = DockWindowMat(win, parent=self.parent, state=state, title=os.path.basename(filename))
+ self.parent.open_dialogs.append(new_dw)
+ new_dw.show()
+ new_dw.saving_state[str].connect(functools.partial(pfs.save_dock_window_to_project, self.parent,
+ self.parent.Defaults.window_type))
+ except:
+ qtutil.critical(filename + " failed to open. Aborting.")
+ return
+
+ def closeEvent(self, event):
+ super().closeEvent(event)
+ self.parent.open_dialogs.remove(self)
+
 
 class Widget(QWidget, WidgetDefault):
  class Labels(WidgetDefault.Labels):
  colormap_index_label = "Choose Colormap:"
+ sb_min_label = "Min colormap range"
+ sb_max_label = "Max colormap range"
 
  class Defaults(WidgetDefault.Defaults):
  colormap_index_default = 1
  roi_list_types_displayed = ['auto_roi', 'roi']
  window_type = 'connectivity_matrix'
+ sb_min_default = -1.00
+ sb_max_default = 1.00
 
  def __init__(self, project, plugin_position, parent=None):
  super(Widget, self).__init__(parent)
@@ -82,7 +155,9 @@ def __init__(self, project, plugin_position, parent=None):
  # item.setData(f['path'], Qt.UserRole)
  # self.roi_list.model().appendRow(item)
  self.cm_comboBox = QtGui.QComboBox(self)
- self.save_pb = QPushButton("&Save matrix windows")
+ self.min_sb = QDoubleSpinBox()
+ self.max_sb = QDoubleSpinBox()
+ self.save_pb = QPushButton("Generate csv files of all open matrices")
  self.load_pb = QPushButton("&Load project matrix windows")
  self.mask_checkbox = QCheckBox("Mask Symmetry")
  self.sem_checkbox = QCheckBox("Use SEM instead of SD")
@@ -125,8 +200,26 @@ def setup_ui(self):
  self.cm_comboBox.addItem("PRGn")
  self.cm_comboBox.addItem("seismic")
  self.vbox.addWidget(self.cm_comboBox)
+ hbox = QHBoxLayout()
+ hbox.addWidget(QLabel(self.Labels.sb_min_label))
+ hbox.addWidget(QLabel(self.Labels.sb_max_label))
+ self.vbox.addLayout(hbox)
+ hbox = QHBoxLayout()
+ hbox.addWidget(self.min_sb)
+ hbox.addWidget(self.max_sb)
+ def min_handler(max_of_min):
+ self.min_sb.setMaximum(max_of_min)
+ def max_handler(min_of_max):
+ self.max_sb.setMinimum(min_of_max)
+ self.min_sb.valueChanged[float].connect(max_handler)
+ self.max_sb.valueChanged[float].connect(min_handler)
+ self.min_sb.setMinimum(-1.0)
+ self.max_sb.setMaximum(1.0)
+ self.min_sb.setSingleStep(0.1)
+ self.max_sb.setSingleStep(0.1)
+ self.vbox.addLayout(hbox)
  self.vbox.addWidget(self.save_pb)
- self.vbox.addWidget(self.load_pb)
+ # self.vbox.addWidget(self.load_pb)
  self.mask_checkbox.setChecked(True)
  self.sem_checkbox.setChecked(False)
  self.vbox.addWidget(self.mask_checkbox)
@@ -144,14 +237,22 @@ def setup_params(self, reset=False):
  self.roi_list.setup_params()
  if len(self.params) == 1 or reset:
  self.update_plugin_params(self.Labels.colormap_index_label, self.Defaults.colormap_index_default)
+ self.update_plugin_params(self.Labels.sb_min_label, self.Defaults.sb_min_default)
+ self.update_plugin_params(self.Labels.sb_max_label, self.Defaults.sb_max_default)
  self.cm_comboBox.setCurrentIndex(self.params[self.Labels.colormap_index_label])
+ self.min_sb.setValue(self.params[self.Labels.sb_min_label])
+ self.max_sb.setValue(self.params[self.Labels.sb_max_label])
 
 
  def setup_param_signals(self):
  super().setup_param_signals()
  self.roi_list.setup_param_signals()
  self.cm_comboBox.currentIndexChanged[int].connect(functools.partial(self.update_plugin_params,
  self.Labels.colormap_index_label))
+ self.min_sb.valueChanged[float].connect(functools.partial(self.update_plugin_params,
+ self.Labels.sb_min_label))
+ self.max_sb.valueChanged[float].connect(functools.partial(self.update_plugin_params,
+ self.Labels.sb_max_label))
 
  def connectivity_triggered(self):
  cm_type = self.cm_comboBox.currentText()
@@ -173,10 +274,11 @@ def callback(x):
  win = ConnectivityDialog(self, roinames, cm_type, progress_callback=callback)
  win.resize(900, 900)
  callback(1)
- win.show()
- self.open_dialogs.append(win)
+ # self.open_dialogs.append(win)
  # todo: add matrices to docks
- dock_window = DockWindow()
+ dock_window = DockWindowMat(win, parent=self)
+ self.open_dialogs.append(dock_window)
+ dock_window.show()
  self.save_open_dialogs_to_csv()
 
  def filedialog(self, name, filters):
@@ -203,7 +305,10 @@ def save_triggered(self):
  if not self.open_dialogs:
  qtutil.info('No correlation matrix windows are open. ')
  return
-
+ self.save_open_dialogs_to_csv()
+ qtutil.info('csvs saved to project directory')
+ return
+ #todo: improve general user experience (saving,loading etc). Look at below
  continue_msg = "All Correlation Matrices will be closed after saving, *including* ones you have not saved. \n" \
  "\n" \
  "Continue?"
@@ -242,7 +347,8 @@ def save_triggered(self):
 
  # Now save the actual file
  title = os.path.basename(pickle_path)
- matrix_output_data = (title, dialog.model.roinames, dialog.model._data)
+ matrix_output_data = (title, dialog.connectivity_dialog.model.roinames,
+ dialog.connectivity_dialog.model._data)
  try:
  with open(pickle_path, 'wb') as output:
  pickle.dump(matrix_output_data, output, -1)
@@ -308,7 +414,8 @@ def save_open_dialogs_to_csv(self):
  return
 
  for i, dialog in enumerate(self.open_dialogs):
- rois_names = [dialog.model.rois[x].name for x in range(len(dialog.model.rois))]
+ rois_names = [dialog.connectivity_dialog.model.rois[x].name for x in range(
+ len(dialog.connectivity_dialog.model.rois))]
  file_name_avg = os.path.splitext(os.path.basename(dialog.windowTitle()))[0] + \
  '_averaged_correlation_matrix.csv'
  file_name_stdev = os.path.splitext(os.path.basename(dialog.windowTitle()))[0] + \
@@ -317,17 +424,17 @@ def save_open_dialogs_to_csv(self):
  with open(os.path.join(self.project.path, file_name_avg), 'w', newline='') as csvfile:
  writer = csv.writer(csvfile, delimiter=',')
  writer.writerow(rois_names)
- for row_ind in range(len(dialog.model._data)):
- row = dialog.model._data[row_ind]
+ for row_ind in range(len(dialog.connectivity_dialog.model._data)):
+ row = dialog.connectivity_dialog.model._data[row_ind]
  row = [row[x][0] for x in range(len(row))]
  writer.writerow(row)
  writer.writerow(['Selected videos:']+self.selected_videos)
  # Do the standard deviation
  with open(os.path.join(self.project.path, file_name_stdev), 'w', newline='') as csvfile:
  writer = csv.writer(csvfile, delimiter=',')
  writer.writerow(rois_names)
- for row_ind in range(len(dialog.model._data)):
- row = dialog.model._data[row_ind]
+ for row_ind in range(len(dialog.connectivity_dialog.model._data)):
+ row = dialog.connectivity_dialog.model._data[row_ind]
  row = [row[x][1] for x in range(len(row))]
  writer.writerow(row)
  writer.writerow(['Selected videos:'] + self.selected_videos)
@@ -356,6 +463,7 @@ def setup_whats_this(self):
 class ConnectivityModel(QAbstractTableModel):
  def __init__(self, widget, roinames, cm_type, loaded_data=None, progress_callback=None):
  super(ConnectivityModel, self).__init__()
+ self.widget = widget
  self.cm_type = cm_type
  self.roinames = roinames
 
@@ -422,7 +530,6 @@ def __init__(self, widget, roinames, cm_type, loaded_data=None, progress_callbac
  if progress_callback:
  progress_callback((i*j) / (len(avg_data) * len(avg_data)))
  avg_data[i][j] = (avg_data[i][j], stdev_dict[(i, j)])
-
  self._data = avg_data
  assert(avg_data != [])
 
@@ -439,9 +546,12 @@ def data(self, index, role):
  elif role == Qt.BackgroundRole:
  value = float(tup[0])
 
- gradient_range = matplotlib.colors.Normalize(-1.0, 1.0)
+ min_label = self.widget.min_sb.value()
+ max_label = self.widget.max_sb.value()
+ gradient_range = matplotlib.colors.Normalize(min_label, max_label)
+ cm_type = self.widget.cm_comboBox.currentText()
  cmap = matplotlib.cm.ScalarMappable(
- gradient_range, plt.get_cmap(self.cm_type))
+ gradient_range, plt.get_cmap(cm_type))
  color = cmap.to_rgba(value, bytes=True)
  # color = plt.cm.jet(value)
  # color = [x * 255 for x in color]
@@ -475,12 +585,19 @@ def __init__(self, widget, roinames, cm_type, loaded_data=None, progress_callbac
  self.table.setModel(self.model)
 
  # view.setAspectLocked(True)
- win = pg.GraphicsWindow()
- l = GradientLegend(-1.0, 1.0, cm_type)
- win.setFixedSize(l.labelsize)
- view = win.addViewBox()
- l.setParentItem(view)
- win.setParent(self)
+ #todo: add GradientLegend
+ min_label = widget.min_sb.value()
+ max_label = widget.max_sb.value()
+ l = GradientLegend(min_label, max_label, cm_type)
+ # l.show()
+ # win = pg.GraphicsWindow()
+ # win.setFixedSize(l.labelsize)
+ # view = win.addViewBox()
+ # view.addItem(l)
+ # l.setParentItem(view)
+ # win.show()
+ # win.setParent(self)
+
 
  def setup_ui(self):
  vbox = QVBoxLayout()