before merge j-dev 20250116

src/pymapmanager/interface2/core/search_widget.py

@@ -169,6 +169,19 @@ def data(self, index, role) -> str:
 
         Returns the data stored under the given role for the item referred to by the index. (in str form)
         """
+
+        # abb adding segment color
+        if role == Qt.BackgroundRole:
+            row = index.row()
+            col = index.column()
+            # Get the corresponding row within the actual dataframe
+            # They could be different values due to deleting
+            rowLabel = self._data.index.tolist()[row]
+            # logger.warning(f'row:{row} rowLabel:{rowLabel}')
+            if col==0 and rowLabel == 3:
+                _color = QtGui.QColor('#38ff2a')
+                return QtGui.QBrush(_color) 
+
         # print("data", self.rowCount(None))
         # print("role: ", type(role))
         if role == Qt.DisplayRole:

src/pymapmanager/interface2/mainMenus.py

@@ -3,8 +3,9 @@
 from qtpy import QtWidgets
 
 from pymapmanager._logger import logger, setLogLevel
-from pymapmanager.interface2.stackWidgets import stackWidget2
-from pymapmanager.interface2.mapWidgets import mapWidget
+# from pymapmanager.interface2.stackWidgets import stackWidget2
+from pymapmanager.interface2.stackWidgets.base.mmWidget2 import mmWidget2
+from pymapmanager.interface2.mapWidgets.mapWidget import mapWidget
 
 class PyMapManagerMenus:
     """Main app menus including loaded map and stack widgets.
@@ -304,7 +305,7 @@ def _refreshEditMenu(self):
 
         # from pymapmanager.interface2.stackWidgets import stackWidget2
         frontWindow = self.getApp().getFrontWindow()
-        if isinstance(frontWindow, (stackWidget2, mapWidget)):
+        if isinstance(frontWindow, (mmWidget2, mapWidget)):
             nextUndo = frontWindow.getUndoRedo().nextUndoStr()
             nextRedo = frontWindow.getUndoRedo().nextRedoStr()
             enableUndo = frontWindow.getUndoRedo().numUndo() > 0
@@ -418,32 +419,33 @@ def _refreshFileMenu(self):
         # self.fileMenu.addAction(loadFolderAction)
         # self.fileMenu.addSeparator()
 
-        # abj
-        enableUndo = False
-        enableRedo = False
-        isDirty = False
+        # enableUndo = False
+        # enableRedo = False
+        enableSave = False
 
         frontWindow = self.getApp().getFrontWindow()
 
-        if isinstance(frontWindow, stackWidget2):
-            enableUndo = frontWindow.getUndoRedo().numUndo() > 0
-            enableRedo = frontWindow.getUndoRedo().numRedo() > 0
-            isDirty = frontWindow.getDirty()
-            logger.info(f"isDirty: {isDirty}")
+        if isinstance(frontWindow, (mmWidget2, mapWidget)):
+            if frontWindow.getPath().endswith('.mmap.zip'):
+                enableSave = False
+            else:
+                # enableUndo = frontWindow.getUndoRedo().numUndo() > 0
+                # enableRedo = frontWindow.getUndoRedo().numRedo() > 0
+                enableSave = frontWindow.getDirty()
 
         # save
         saveFileAction = QtWidgets.QAction("Save", self.getApp())
         saveFileAction.setCheckable(False)  # setChecked is True by default?
         saveFileAction.setShortcut("Ctrl+S")
         # saveFileAction.setEnabled(enableUndo and isDirty)
-        saveFileAction.setEnabled(isDirty)
+        saveFileAction.setEnabled(enableSave)
         saveFileAction.triggered.connect(self.getApp().saveFile)
         self.fileMenu.addAction(saveFileAction)
 
         # save as
         saveAsFileAction = QtWidgets.QAction("Save As", self.getApp())
         saveAsFileAction.setCheckable(False)  # setChecked is True by default?
-        saveAsFileAction.triggered.connect(self.getApp().saveAsFile)
+        saveAsFileAction.triggered.connect(self.getApp().saveAs)
         self.fileMenu.addAction(saveAsFileAction)
 
         self.fileMenu.addSeparator()
@@ -463,16 +465,28 @@ def _refreshFileMenu(self):
         self.settingsMenu.aboutToShow.connect(self._refreshSettingsMenu)
         self.fileMenu.addSeparator()
 
-        #abj
         analysisParametersAction = QtWidgets.QAction('App Analysis Parameters', self.getApp())
         analysisParametersAction.triggered.connect(self.getApp()._showAnalysisParameters)
         self.fileMenu.addAction(analysisParametersAction)
 
         self.fileMenu.addSeparator()
         importNewTIFAction = QtWidgets.QAction('Import new TIF (channel)', self.getApp())
+        importNewTIFAction.setEnabled(isinstance(frontWindow, mmWidget2))
         importNewTIFAction.triggered.connect(self.getApp().importNewTIF)
         self.fileMenu.addAction(importNewTIFAction)
 
+        # open some mapmanagercore sample data (download and store locally with pooch)
+        self.fileMenu.addSeparator()
+        self.sampleDataMenu = QtWidgets.QMenu("Sample Data ...")
+        importList = ['Tiff File Ch1', 'Tiff File Ch2', 'mmap with spines and segments']
+        for importType in importList:
+            loadSampleAction = QtWidgets.QAction(importType, self.getApp())
+            loadSampleAction.triggered.connect(
+                partial(self.getApp().loadSampleData, importType)
+            )
+            self.sampleDataMenu.addAction(loadSampleAction)
+        self.fileMenu.addMenu(self.sampleDataMenu)
+
     def _refreshOpenRecent(self):
         """Dynamically generate the open recent stack/map menu.
         

src/pymapmanager/interface2/mapWidgets/mapTableWidget.py

@@ -1,12 +1,12 @@
+import os
 import sys
 from typing import List, Union  # , Callable, Iterator, Optional
 
 from qtpy import QtGui, QtCore, QtWidgets
 
+from mapmanagercore import IMPORT_FILE_EXTENSIONS
 from pymapmanager.interface2.core.search_widget import myQTableView
-
 from pymapmanager.timeseriesCore import TimeSeriesCore
-
 from pymapmanager._logger import logger
 
 class mapTableWidget(QtWidgets.QWidget):
@@ -29,7 +29,44 @@ def __init__(self, timeSeriesCore : TimeSeriesCore):
 
         self.slot_switchMap(timeSeriesCore)
 
-        # self._setModel()
+        self.setAcceptDrops(True)
+
+    def dragEnterEvent(self, event):
+        """Accept drag/drop of tiff file and append to _timeSeriesCore.
+        """
+        if event.mimeData().hasUrls():
+            urlList = event.mimeData().urls()
+            url = urlList[0]
+            file_path = url.toLocalFile()
+            _path, _ext = os.path.splitext(file_path)
+            if _ext in IMPORT_FILE_EXTENSIONS:
+                event.acceptProposedAction()
+            else:
+                logger.warning(f'did not understand ext "{_ext}" path "{_path}"')
+
+    def dropEvent(self, event):
+        """When user drops a tiff file, append it to the timeseries.
+        """
+        urlList = event.mimeData().urls()
+        url = urlList[0]
+        file_path = url.toLocalFile()
+        # self.label.setText(f"Dropped file: {file_path}")
+        # self._timeSeriesCore.loadInNewChannel(file_path)  # todo specify append (default to tp 0)
+        # append the tiff file to the _timeSeriesCore
+        logger.info(f'file_path:{file_path}')
+        timePoint = self._timeSeriesCore.numSessions
+        channel = 0
+        name = 'xxx imported channel'
+
+        logger.info('adding new timepoint from tif, timePoint:{timePoint}')
+
+        from mapmanagercore.lazy_geo_pd_images.loader.imageio import MultiImageLoader
+        _loader = MultiImageLoader()
+        _loader.read(file_path, time=timePoint, channel=channel, name=name)
+        self._timeSeriesCore._fullMap.loader.merge(_loader)
+
+        # update gui
+        self._setModel()
 
     def slot_switchMap(self, timeSeriesCore : TimeSeriesCore):
         self._timeSeriesCore = timeSeriesCore

src/pymapmanager/interface2/mapWidgets/mapWidget.py

@@ -59,7 +59,6 @@ class mapWidget(MainWindow):
 
     _widgetName = 'Map Widget'
 
-    # def __init__(self, mmMap : pmm.mmMap):
     def __init__(self, timeseriescore : TimeSeriesCore):
         super().__init__(mapWidget=self, iAmMapWidget=True)
 
@@ -77,8 +76,10 @@ def __init__(self, timeseriescore : TimeSeriesCore):
 
         self.setWindowTitle(os.path.split(self._map.path)[1])
 
-    # def getMapSelection(self) -> MapSelection:
-    #     return self._mapSelection
+    # over-ride from mmWIdget2, which returns stack
+    # using this to share some api like save  and save as
+    def getStack(self) -> TimeSeriesCore:
+        return self._map
 
     def zoomToPointAnnotation(self,
                               idx : int,
@@ -102,6 +103,10 @@ def getMap(self):
     def getPath(self):
         return self._map.path
 
+    # over-ride mmWidget2
+    def getDirty(self):
+        return self._map.getDirty()
+
     def emitUndoEvent(self):
         """
         """
@@ -186,6 +191,10 @@ def openStackRun(self,
         if spineID and _multipleTp:
             self.linkOpenPlots(link=True)
 
+    @property
+    def numSessions(self):
+        return self.getMap().numSessions
+
     def getNumSessions(self):
         return self.getMap().numSessions
 

src/pymapmanager/interface2/pyMapManagerApp2.py

@@ -50,9 +50,14 @@ def _importPlugins(pluginType : str, verbose = False):
     elif pluginType == 'mapWidgets':
         _modulePath = 'pymapmanager.interface2.mapWidgets'
         # _folderPath = 'mapWidgets'
-
+    else:
+        logger.error(f'did not understand pluginType:"{pluginType}" expecting one of (stackWidgets, mapWidgets)')
+        return
+
     numAdded = 0
 
+    # logger.warning(f'verbose:{verbose}')
+
     # CRITICAL: abb this list is not complete in pyinstaller
     invalidate_caches()  # ???
     m1 = import_module(_modulePath)
@@ -149,7 +154,7 @@ def loadPlugins(pluginType : str, verbose = False) -> dict:
 
     pluginDict = {}
 
-    _importPlugins(pluginType, pluginType == 'stackWidgets')
+    _importPlugins(pluginType)
 
     if pluginType == 'stackWidgets':
         members = inspect.getmembers(pymapmanager.interface2.stackWidgets)
@@ -336,17 +341,23 @@ def updateMapPathDict(self, aWidget):
         # self.pathDict["lastSaveTime"] = self._timeSeriesCore.getLastSaveTime()
 
         path = aWidget.getPath()
-        refreshTimeSeriesCore = TimeSeriesCore(path)
-        # lastSaveTime = aWidget.getLastSaveTime() # still showing old one, need to create new time series core to refresh?
-        lastSaveTime = refreshTimeSeriesCore.getLastSaveTime()
-        numTimepoints = refreshTimeSeriesCore.numSessions
+
+        # abb why are we making TimeSeriesCore
+        logger.error('do not create TimeSeriesCore')
+
+        lastSaveTime = aWidget.getLastSaveTime() # still showing old one, need to create new time series core to refresh?
+        numTimepoints = aWidget.numSessions
+
+        # refreshTimeSeriesCore = TimeSeriesCore(path)
+        # lastSaveTime = refreshTimeSeriesCore.getLastSaveTime()
+        # numTimepoints = refreshTimeSeriesCore.numSessions
         pathDict = {"Path": path,
                     "Last Save Time": str(lastSaveTime), # needs to be updated
                     "Timepoints": str(numTimepoints)}
         self._app.getConfigDict().addMapPathDict(pathDict)
 
     def save(self, aWidget):
-        # logger.info(f'TODO: save widget: {aWidget}')
+        # abb only stackwidget2 has save(), e.g. map widgets do not
         logger.info(f'save widget: {aWidget}')
         aWidget.save()
 
@@ -356,10 +367,11 @@ def save(self, aWidget):
         # self.pathDict["lastSaveTime"] = lastSaveTime
 
     def saveAs(self, aWidget):
-        # logger.info(f'TODO: save as widget: {aWidget}')
+        # abb only stackwidget2 has fileSaveAs(), e.g. map widgets do not
         logger.info(f'save as widget: {aWidget}')
-        aWidget.fileSaveAs()
-        self.updateMapPathDict(aWidget) # abj
+        _saved = aWidget.saveAs()
+        if _saved:
+            self.updateMapPathDict(aWidget) # abj
 
     def _checkWidgetExists(self, path):
         """ Check if a widget exists in the widget dict list
@@ -587,7 +599,7 @@ def saveFile(self):
         _frontWidget = self.getFrontWindow()
         self._openWidgetList.save(_frontWidget)
 
-    def saveAsFile(self):
+    def saveAs(self):
         """ Save as a new file
         """
         _frontWidget = self.getFrontWindow()
@@ -666,6 +678,28 @@ def getScreenGrid(self, numItems : int, itemsPerRow : int) -> List[List[int]]:
     def getOpenWidgetDict(self):
         return self._openWidgetList.getDict()
 
+    def loadSampleData(self, sampleName):
+        if sampleName == 'Tiff File Ch1':
+            import mapmanagercore.data
+            from mapmanagercore.data import getTiffChannel_1
+            tiffPath = getTiffChannel_1()
+            if os.path.isfile(tiffPath):
+                self.loadStackWidget(tiffPath)
+        elif sampleName == 'Tiff File Ch2':
+            import mapmanagercore.data
+            from mapmanagercore.data import getTiffChannel_2
+            tiffPath = getTiffChannel_2()
+            if os.path.isfile(tiffPath):
+                self.loadStackWidget(tiffPath)
+        elif sampleName == 'mmap with spines and segments':
+            import mapmanagercore.data
+            from mapmanagercore.data import getSingleTimepointMap
+            tiffPath = getSingleTimepointMap()
+            if os.path.isfile(tiffPath):
+                self.loadStackWidget(tiffPath)
+        else:
+            logger.warning(f'did not understand "{sampleName}"')
+
     def loadStackWidget(self, path : str = None) -> Union[stackWidget2, mapWidget]:
         """Load a stack from a path and open a stackWidget2 or mapWidget
 
@@ -690,7 +724,7 @@ def loadStackWidget(self, path : str = None) -> Union[stackWidget2, mapWidget]:
 
             dialog = QtWidgets.QFileDialog(None)
             # dialog.setFileMode(QtWidgets.QFileDialog.Directory)
-            dialog.setNameFilter("zarr directory (*.mmap)")
+            dialog.setNameFilter("MapManager Files (*.mmap, *.zip)")
             # openFilePath = dialog.getExistingDirectory(None)
             # dialog.setOptions(options)
             openFilePath = dialog.getExistingDirectory()
@@ -701,11 +735,11 @@ def loadStackWidget(self, path : str = None) -> Union[stackWidget2, mapWidget]:
             _ext = os.path.splitext(openFilePath)[1]
             window = self.activeWindow() 
             if openFilePath == "":
-                logger.warning("openFilePath is Empty")
+                # logger.warning("openFilePath is Empty")
                 # QtWidgets.QMessageBox.critical(window, "Error", "File Path is Empty")
                 return
-            elif _ext != '.mmap': # could make this into a for loop until user inputs .mmap
-                logger.warning(f"incorrect directory type, must be of extension: (.mmap)") 
+            elif _ext not in ['.mmap', '.zip']: # could make this into a for loop until user inputs .mmap
+                logger.warning(f"incorrect directory type, must be of extension: .mmap or .zip") 
                 QtWidgets.QMessageBox.critical(window, "Error", "Incorrect directory type, must be of extension: (.mmap)")
                 return
 
@@ -804,9 +838,11 @@ def clearRecentFiles(self):
         self._openFirstWindow.refreshUI()
 
     def importNewTIF(self):
-        pass
 
         frontStackWindow = self.getFrontWindow()
+        if not isinstance(frontStackWindow, stackWidget2):
+            return
+
         # bring up directory
 
         # get newTifPath

src/pymapmanager/interface2/runInterfaceBob.py

@@ -12,7 +12,7 @@ def run():
     app = PyMapManagerApp(sys.argv)
 
     # open a single timepoint map with segments and spines
-    path = mapmanagercore.data.getSingleTimepointMap()
+    # path = mapmanagercore.data.getSingleTimepointMap()
 
     # a single timepoint tif file (import)
     # path = mapmanagercore.data.getTiffChannel_1()
@@ -33,7 +33,7 @@ def run():
 
     # a mmap with multiple timepoints, connects segments and spines
     # path = '/Users/cudmore/Desktop/multi_timepoint_map_seg_spine_connected.mmap'
-    # path = mapmanagercore.data.getMultiTimepointMap()
+    path = mapmanagercore.data.getMultiTimepointMap()
 
     # path = '/Users/cudmore/Desktop/yyy4.mmap'
     # path = '/Users/cudmore/Desktop/single_timepoint.mmap'