Merge branch 'johnson-dev' into cudmore-dev

pymapmanager/annotations/baseAnnotationsCore.py

@@ -6,7 +6,11 @@
 import pandas as pd
 import shapely
 
+import mapmanagercore
 from mapmanagercore import MapAnnotations
+# from mapmanagercore import MapAnnotations, MultiImageLoader
+# from mapmanagercore.annotations.single_time_point.base import SingleTimePointFrame
+# from mapmanagercore import single_time_point
 from mapmanagercore.layers.line import clipLines
 from mapmanagercore.lazy_geo_pandas import LazyGeoFrame
 
@@ -89,8 +93,12 @@ def getSegmentPlot(self, segmentID,
         _stopSlice = zSlice + zPlusMinus
 
         df = self.getDataFrame()
+        # logger.info(f"df: {df}")
         df['rowIndex'] = list(np.arange(len(df)))
-        df = df[(df['z']>=_startSlice) & (df['z']<=_stopSlice)]
+
+        #abj: 7/17/24
+        if not df.empty:
+            df = df[(df['z']>=_startSlice) & (df['z']<=_stopSlice)]
 
         return df
 
@@ -165,6 +173,10 @@ def moveSpine(self, spineID :int, x, y, z):
         # _moved = self._fullMap.moveSpine((spineID, self.sessionID), x=x, y=y, z=z)
         _moved = self._fullMap.moveSpine(spineID, x=x, y=y, z=z)
 
+        #abj: 7/5
+        #update background ROI
+        self._fullMap.snapBackgroundOffset(spineID)
+
         # rebuild df from mutated full map
         self._buildDataFrame()
 
@@ -252,17 +264,22 @@ def _buildDataFrame(self):
         """
 
         # _startSec = time.time()
-
+        # logger.info(f"self._fullMap.points {self._fullMap.points}")
+        # logger.info(f"type self._fullMap.points {type(self._fullMap.points)}")
         try:
             allSpinesDf = self._fullMap.points[:]
         except (KeyError) as e:
             logger.warning(e)
             return
 
-        # add (x, y) if it does not exists
-        xyCoord = allSpinesDf['point'].get_coordinates()
-        allSpinesDf['x'] = xyCoord['x']
-        allSpinesDf['y'] = xyCoord['y']
+        #abj: check if points are empty:
+        if len(allSpinesDf) > 0:
+            logger.info(f"allSpinesDf {type(allSpinesDf)}") # <class 'geopandas.geodataframe.GeoDataFrame'>
+            # logger.info(f"allSpinesDf['point'] {type(allSpinesDf['point'])}")
+            # add (x, y) if it does not exists
+            xyCoord = allSpinesDf['point'].get_coordinates()
+            allSpinesDf['x'] = xyCoord['x']
+            allSpinesDf['y'] = xyCoord['y']
 
         allSpinesDf['roiType'] = 'spineROI'
         allSpinesDf.insert(0,'index', allSpinesDf.index)  # index is first column
@@ -295,6 +312,11 @@ def getSpineLines(self):
         1        382.0  250.0 NaN
         """
         # anchorDf = self._sessionMap['anchors'].get_coordinates(include_z=True)
+
+        # test= self._fullMap.points['anchorLine']
+        # logger.info(f"getSpineLines test {test}")
+        # logger.info(f"getSpineLines test type {type(test)}")
+
         anchorDf = self._fullMap.points['anchorLine'].get_coordinates(include_z=True)
 
         # for undo delete, we need to re-assing row lables to match points self._df

pymapmanager/interface2/mainMenus.py

@@ -49,6 +49,20 @@ def _buildMenus(self, mainMenu, mainWindow):
 
         fileMenu.addSeparator()
 
+        # abj
+        saveFileAction = QtWidgets.QAction("Save", self.getApp())
+        saveFileAction.setCheckable(False)  # setChecked is True by default?
+        saveFileAction.setShortcut("Ctrl+S")
+        saveFileAction.triggered.connect(self.getApp().saveFile)
+        fileMenu.addAction(saveFileAction)
+
+        saveAsFileAction = QtWidgets.QAction("Save As", self.getApp())
+        saveAsFileAction.setCheckable(False)  # setChecked is True by default?
+        saveAsFileAction.triggered.connect(self.getApp().saveAsFile)
+        fileMenu.addAction(saveAsFileAction)
+
+        fileMenu.addSeparator()
+
         # open recent (submenu) will show two lists, one for files and then one for folders
         self.openRecentMenu = QtWidgets.QMenu("Open Recent ...")
         self.openRecentMenu.aboutToShow.connect(self._refreshOpenRecent)
@@ -130,7 +144,7 @@ def _buildMenus(self, mainMenu, mainWindow):
                 self._helpMenuAction = _action
 
         return self._helpMenuAction
-    
+
     def _refreshPluginsMenu(self):
         logger.info('re-create plugin menu with available pligins')
 

pymapmanager/interface2/openFirstWindow.py

@@ -25,7 +25,7 @@ class OpenFirstWindow(MainWindow):
     def __init__(self, pyMapManagerApp : PyMapManagerApp, parent=None):
         super().__init__(parent)
 
-        # self._app = pyMapManagerApp
+        self._app = pyMapManagerApp
 
         self.recentStackList = self.getApp().getConfigDict().getRecentStacks()
         self.recentMapList = self.getApp().getConfigDict().getRecentMaps()
@@ -160,6 +160,13 @@ def _buildUI(self):
         aButton.clicked.connect(partial(self._on_open_button_click, name))
         hBoxLayout.addWidget(aButton, alignment=QtCore.Qt.AlignLeft)
 
+        name = 'Drag and Drop'
+        aButton = DragAndDropWidget(name, self._app)
+        aButton.setFixedSize(QtCore.QSize(200, 60))
+        aButton.setToolTip('Drag and Drop Tif File.')
+        # aButton.clicked.connect(partial(self._on_open_button_click, name))
+        hBoxLayout.addWidget(aButton, alignment=QtCore.Qt.AlignLeft)
+
         # recent files and tables
         recent_vBoxLayout = QtWidgets.QVBoxLayout()
 
@@ -185,6 +192,33 @@ def _buildUI(self):
 
         _mainVLayout.addLayout(recent_vBoxLayout)
 
+# QtWidgets.QPushButton
+# QtWidgets.QMainWindow
+class DragAndDropWidget(QtWidgets.QPushButton):
+    def __init__(self, name, app: PyMapManagerApp):
+        super().__init__(name)
+        self.setWindowTitle("Drag and Drop")
+        self.resize(720, 480)
+        self.setAcceptDrops(True)
+
+        self._app = app
+
+    def dragEnterEvent(self, event):
+        if event.mimeData().hasUrls():
+            event.accept()
+        else:
+            event.ignore()
+
+    def dropEvent(self, event):
+        files = [u.toLocalFile() for u in event.mimeData().urls()]
+        for tifFile in files:
+            # print(f)
+            logger.info(f"loading file {tifFile}")
+            self._app.loadTifFile(tifFile)
+            # Create new image loader iwth path
+            # emit f = path to file
+
+
 def test():
     import sys
     from sanpy.interface import SanPyApp

pymapmanager/interface2/pyMapManagerApp2.py

@@ -294,6 +294,43 @@ def openTimeSeries(self):
         logger.info('')
         pass
 
+    def saveFile(self):
+        """ Save new changes to current file
+        """
+        # zarrPath = self.stackWidget.getStack().getPath()
+        # <pymapmanager.interface2.stackWidgets.stackWidget2.stackWidget2 object at 0x00000194F144C790>
+        # temp = self._stackWidgetDict['\\Users\\johns\\Documents\\GitHub\\MapManagerCore\\data\\rr30a_s0u.mmap']
+        # logger.info(f'Saving file at path: {temp}')
+
+        logger.info(f'Saving file at path: {  self._stackWidgetDict.keys()}')
+        for key in self._stackWidgetDict.keys():
+            # looping through every path in stackWidgetDict
+            # key = path of current stack
+            stackWidget = self._stackWidgetDict[key]
+            stackWidget.save(key)
+
+    def saveAsFile(self):
+        """ Save change to a new file
+
+        2 Scenarios:
+            1.) mmap file has not been created yet and we need to save a new one
+            2.) There is already a mmap file and user wants to create a new one
+                - in this scenario, after creating a new one, save would still save on the old one,
+                until user loads in that new file
+        """
+        logger.info(f'Saving as file {  self._stackWidgetDict.keys()}')
+
+        # scenario 1) Should be called when something is dragged and dropped, new file is loaded in
+        # this is handled in loadTifFile
+        # scenario 2) 
+        if len(self._stackWidgetDict) > 0:
+            for key in self._stackWidgetDict.keys():
+                # looping through every path in stackWidgetDict
+                # key = path of current stack
+                stackWidget = self._stackWidgetDict[key]
+                stackWidget.fileSaveAs()
+                # stackWidget.saveAs(key)
+
     def _undo_action(self):
         self.getFrontWindow().emitUndoEvent()
 
@@ -357,6 +394,58 @@ def loadMapWidget(self, path):
 
         return self._mapWidgetDict[path]
 
+    def loadTifFile(self, path : str):
+        """Load a stack from tif from a path.
+        Only happens on first load/ drag and drop
+        Create stackwidget/ mmap from tif file
+        
+        Parameters
+        ----------
+        path : str
+            Full path to tif file
+        """
+        from mapmanagercore import MapAnnotations, MultiImageLoader
+        from mapmanagercore.lazy_geo_pandas import LazyGeoFrame
+        from mapmanagercore.schemas import Segment, Spine
+
+        loader = MultiImageLoader()
+        # path = "C:\\Users\\johns\\Documents\\GitHub\\PyMapManager-Data\\one-timepoint\\rr30a_s0_ch1.tif"
+
+        try: # Check if path is a tif file
+            # TODO: detect channel, move channel to parameter
+            loader.read(path, channel=0)
+            logger.info("loading tif file!")
+        except Exception as e: # else return error message
+            logger.info(f"Exeception when reading tif file: {e}")
+            return
+        import pandas as pd
+        import geopandas
+        lineSegments = geopandas.GeoDataFrame()
+        points = geopandas.GeoDataFrame()
+
+
+        # Might no be necessary, example.ipynb works with empty geodataframes
+        # self._segments = LazyGeoFrame(
+        #     Segment, data=lineSegments, store=self)
+        # self._points = LazyGeoFrame(Spine, data=points, store=self)
+
+        map = MapAnnotations(loader.build(),
+                            lineSegments=lineSegments,
+                            points=points)
+
+        # Save new mmap file in same directory as tif file
+        import os
+        pathParse = os.path.splitext(path)[0] # without extension
+        newMapPath = pathParse + ".mmap"
+        logger.info("Save new Map from tif file")
+        map.save(newMapPath)
+
+        self.loadStackWidget(newMapPath)
+        # map.points[:]
+        # need to save zarr file first. so that we can create a stack from it within stackwidget
+        # need to create stackwidget from new map
+        #only save when user clicks save as
+
     def loadStackWidget(self, path : str):
         """Load a stack from a path.
         

pymapmanager/interface2/runInterfaceJohnson.py

@@ -26,8 +26,11 @@ def run():
     # path = '../PyMapManager-Data/core-map/one-timepoint/oneTimepoint.mmap'
     # path ='\\Users\\johns\\Documents\\GitHub\\MapManagerCore\\sandbox\\data\\rr30a_s0.mmap'
     # path = 'C:\\Users\\johns\\Documents\\GitHub\\MapManagerCore\\data\\rr30a_s0u.mmap'
-    path = '\\Users\\johns\\Documents\\GitHub\\MapManagerCore\\data\\rr30a_s0u.mmap'
-
+    # path = '\\Users\\johns\\Documents\\GitHub\\MapManagerCore\\data\\rr30a_s0u.mmap'
+    path = '/Users/johns/Documents/GitHub/MapManagerCore/data/rr30a_s0u.mmap'
+    # path = '/Users/johns/Documents/GitHub/PyMapManager-Data/one-timepoint/rr30a_s0_ch1.mmap'
+    # import mapmanagercore
+    # path = mapmanagercore.getSingleTimepointMap()
     sw2 = app.loadStackWidget(path)
 
     df = sw2.getStack().getPointAnnotations().getDataFrame()
@@ -40,5 +43,14 @@ def run():
 
     sys.exit(app.exec_())
 
+def run2():
+    app = PyMapManagerApp()
+    # path = '/Users/johns/Documents/GitHub/PyMapManager-Data/one-timepoint/rr30a_s0_ch1.tif'
+    path = '/Users/johns/Documents/GitHub/PyMapManager-Data/one-timepoint/rr30a_s0_ch1.mmap'
+    # sw2 = app.loadTifFile(path)
+    sw2 = app.loadStackWidget(path)
+    sys.exit(app.exec_())
+
 if __name__ == '__main__':
-    run()
+    run()
+    # run2()