feat: Tracer functionality

.gitignore

@@ -10,6 +10,7 @@
 *\#
 *~
 *.egg
+*.egg-info/
 .eggs/
 build
 dist

CellProfiler-Analyst.iss

@@ -0,0 +1,42 @@
+; Script generated by the Inno Setup Script Wizard.
+; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
+
+[Setup]
+; NOTE: The value of AppId uniquely identifies this application.
+; Do not use the same AppId value in installers for other applications.
+; (To generate a new GUID, click Tools | Generate GUID inside the IDE.)
+AppId={{7DC05C02-41F1-4241-BD72-449D12360372}
+AppName=CellProfiler-Analyst
+AppVersion=Tracer
+;AppVerName=CellProfiler-Analyst Tracer
+AppPublisher=Broad Institute
+AppPublisherURL=http://cellprofiler.org
+AppSupportURL=http://cellprofiler.org
+AppUpdatesURL=http://cellprofiler.org
+DefaultDirName={pf64}\CellProfiler-Analyst
+DefaultGroupName=CellProfiler-Analyst
+LicenseFile=.\LICENSE
+OutputDir=.\output
+OutputBaseFilename=CellProfiler-Analyst
+SetupIconFile=.\cpa\icons\cpa.ico
+Compression=lzma
+SolidCompression=yes
+
+[Languages]
+Name: "english"; MessagesFile: "compiler:Default.isl"
+
+[Tasks]
+Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"; Flags: unchecked
+
+[Files]
+Source: ".\dist\CellProfiler-Analyst.exe"; DestDir: "{app}"; Flags: ignoreversion
+Source: ".\dist\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
+; NOTE: Don't use "Flags: ignoreversion" on any shared system files
+
+[Icons]
+Name: "{group}\CellProfiler-Analyst"; Filename: "{app}\CellProfiler-Analyst.exe"
+Name: "{commondesktop}\CellProfiler-Analyst"; Filename: "{app}\CellProfiler-Analyst.exe"; Tasks: desktopicon
+
+[Run]
+Filename: "{app}\CellProfiler-Analyst.exe"; Description: "{cm:LaunchProgram,CellProfiler-Analyst}"; Flags: nowait postinstall skipifsilent
+

CellProfiler-Analyst.py

@@ -5,7 +5,6 @@
 # =============================================================================
 
 
-
 import sys
 import os
 import os.path
@@ -21,6 +20,7 @@
 from cpa.plateviewer import PlateViewer
 from cpa.imageviewer import ImageViewer
 from cpa.imagegallery import ImageGallery
+from cpa.tracer import Tracer
 from cpa.boxplot import BoxPlot
 from cpa.scatter import Scatter
 from cpa.histogram import Histogram
@@ -55,7 +55,6 @@ def emit(self, record):
     else:
         p.LoadFile(sys.argv[1])
 
-
 from cpa.cpatool import CPATool
 import inspect
 
@@ -74,6 +73,7 @@ def emit(self, record):
 ID_BOXPLOT = wx.NewIdRef()
 ID_DIMENSREDUX = wx.NewIdRef()
 ID_NORMALIZE = wx.NewIdRef()
+ID_TRACER = wx.NewIdRef()
 
 def get_cpatool_subclasses():
     '''returns a list of CPATool subclasses.
@@ -115,6 +115,7 @@ def __init__(self, properties, parent, id=-1, **kwargs):
         tb.AddTool(ID_BOXPLOT.GetId(), 'Box Plot', get_icon("boxplot").ConvertToBitmap(), shortHelp='Box Plot')
         tb.AddTool(ID_DIMENSREDUX.GetId(), 'Reduction', get_icon("dimensionality").ConvertToBitmap(), shortHelp='Dimensionality Reduction')
         tb.AddTool(ID_TABLE_VIEWER.GetId(), 'Table Viewer', get_icon("data_grid").ConvertToBitmap(), shortHelp='Table Viewer')
+        tb.AddTool(ID_TRACER.GetId(), 'Tracer', get_icon("tracer").ConvertToBitmap(), shortHelp='Tracer')
         # tb.AddLabelTool(ID_NORMALIZE, 'Normalize', get_icon("normalize").ConvertToBitmap(), shortHelp='Normalization Tool', longHelp='Launch Feature Normalization Tool')
         tb.Realize()
 
@@ -147,6 +148,7 @@ def __init__(self, properties, parent, id=-1, **kwargs):
         dimensionMenuItem   = toolsMenu.Append(ID_DIMENSREDUX, 'Dimensionality Reduction', helpString='Launches the Dimensionality Reduction tool.')
         dataTableMenuItem   = toolsMenu.Append(ID_TABLE_VIEWER, 'Table Viewer\tCtrl+Shift+T', helpString='Launches the Table Viewer tool.')
         normalizeMenuItem   = toolsMenu.Append(ID_NORMALIZE, 'Normalization Tool\tCtrl+Shift+T', helpString='Launches a tool for generating normalized values for measurement columns in your tables.')
+        tlmMenuItem         = toolsMenu.Append(ID_TRACER, 'Tracer\tCtrl+Shift+L', helpString='Launches the Tracer time-lapse viewer tool.')
         self.GetMenuBar().Append(toolsMenu, 'Tools')
 
         logMenu = wx.Menu()
@@ -212,6 +214,7 @@ def update(x):
         self.Bind(wx.EVT_TOOL, self.launch_histogram_plot, id=ID_HISTOGRAM)
         self.Bind(wx.EVT_TOOL, self.launch_density_plot, id=ID_DENSITY)
         self.Bind(wx.EVT_TOOL, self.launch_box_plot, id=ID_BOXPLOT)
+        self.Bind(wx.EVT_TOOL, self.launch_tracer, id=ID_TRACER)
         self.Bind(wx.EVT_TOOL, self.launch_dimens_redux, id=ID_DIMENSREDUX)
         self.Bind(wx.EVT_TOOL, self.launch_normalization_tool, id=ID_NORMALIZE)
         self.Bind(wx.EVT_MENU, self.on_close, self.exitMenuItem)
@@ -268,6 +271,10 @@ def launch_image_gallery(self, evt=None):
             colViewer = ImageGallery(parent=self, properties=self.properties)
             colViewer.Show(True)
 
+    def launch_tracer(self, evt=None):
+        tracer = Tracer(parent=self)
+        tracer.Show(True)        
+
     def launch_box_plot(self, evt=None):
         if self.confirm_properties():
             boxplot = BoxPlot(parent=self)
@@ -429,7 +436,6 @@ def on_idle(self, evt=None):
             self.console.AppendText(self.log_text)
             self.log_text = ''
 
-
 class CPAnalyst(wx.App):
     '''The CPAnalyst application.
     This launches the main UI, and keeps track of the session.

cpa/boxplot.py

@@ -208,8 +208,6 @@ def save_settings(self):
                 'filter' : self.filter_choice.Value,
                 'x-lim'  : self.figpanel.subplot.get_xlim(),
                 'y-lim'  : self.figpanel.subplot.get_ylim(),
-##                'grouping': self.group_choice.Value,
-##                'version': '1',
                 }
 
     def load_settings(self, settings):
@@ -218,9 +216,6 @@ def load_settings(self, settings):
         settings - a dictionary mapping setting names to values encoded as
                    strings.
         '''
-##        if 'version' not in settings:
-##            settings['grouping'] = NO_GROUP
-##            settings['version'] = '1'
         if 'table' in settings:
             self.table_choice.SetStringSelection(settings['table'])
             self.update_column_fields()

cpa/columnfilter.py

@@ -23,9 +23,13 @@ def __init__(self, parent, tables, allow_delete=True, expression=None, **kwargs)
         self.tables = tables
         self.types = {}
         self.types[p.image_table] = db.GetColumnTypes(p.image_table)
+        self.types[p.object_table] = db.GetColumnTypes(p.object_table)
         self.tableChoice = ComboBox(self, choices=self.tables, size=(150,-1), style=wx.CB_READONLY)
         self.tableChoice.Select(0)
-        self.colChoice = ComboBox(self, choices=db.GetColumnNames(p.image_table), size=(150,-1), style=wx.CB_READONLY)
+        choices = []
+        for table in tables:
+            choices += db.GetColumnNames(table)
+        self.colChoice = ComboBox(self, choices=choices, size=(150,-1), style=wx.CB_READONLY)
         self.colChoice.Select(0)
         self.comparatorChoice = ComboBox(self, size=(80,-1), style=wx.CB_READONLY)
         self.update_comparator_choice()

cpa/dbconnect.py

@@ -1290,7 +1290,7 @@ def GetCellDataForRedux(self):
         if not all([type(x) in valid_types for x in data[0]]):
             raise ValueError("Invalid column types were found in the data. "
                              "Only numerical columns can be present in the object table")
-        return np.array(data, dtype=np.float)
+        return np.array(data, dtype='float')
 
     def GetCellData(self, obKey):
         '''

cpa/dimensionreduction.py

@@ -810,7 +810,7 @@ def update_figpanel(self, evt=None):
             start = time()
 
             dlg.Pulse('Generating model and plot')
-            selected_method = self.method_choice.GetStringSelection()
+            selected_method = self.method_choice.GetValue()
             selected_plot = self.plot_choice.GetStringSelection()
 
             if self.figpanel.calculated != selected_method:

cpa/fastgentleboosting.py

@@ -391,6 +391,7 @@ def XValidate(self, colnames, num_learners, label_matrix, values, folds, group_l
             holdout_results = self.Train(colnames, num_learners, holdin_labels, holdin_values, test_values=holdout_values)
             if holdout_results is None:
                 return None
+
             # pad the end of the holdout set with the last element
             if len(holdout_results) < num_learners:
                 holdout_results += [holdout_results[-1]] * (num_learners - len(holdout_results))