added olsen nd2

sandbox/qt-plotly/myPlot.py

@@ -7,6 +7,12 @@
 
 from IPython.display import display
 
+"""
+Requires
+    pip install PyQtWebEngine
+    pip install ipywidgets
+"""
+
 def plot():
     # fig = go.Figure(data=[go.Scattergl(x=[1, 2, 3], y=[4, 5, 6])])
     x=[1, 2, 3]
@@ -20,7 +26,7 @@ def plot():
 
 out = Output()
 
-class Backend(QtCore.QObject):
+class myBackend(QtCore.QObject):
     pointChanged = QtCore.Signal(float, float)
 
     # @QtCore.Signal(float,float)
@@ -34,7 +40,7 @@ def __init__(self, parent=None):
 
         # self.button = QtWidgets.QPushButton('Plot', self)
         # self.browser = QtWebEngineWidgets.QWebEngineView(self)
-        self.browser = QtWebEngineWidgets.QWebEngineView()
+        self.browser: QtWebEngineWidgets.QWebEngineView = QtWebEngineWidgets.QWebEngineView()
 
         # self.vlayout = QtWidgets.QVBoxLayout(self)
         # self.vlayout.addWidget(self.button, alignment=QtCore.Qt.AlignHCenter)
@@ -55,20 +61,23 @@ def onPointChanged(self, x, y):
     def plot2(self):
         # map_view = QtWebEngineWidgets.QWebEngineView()
 
-        backend = Backend(self)
+        backend = myBackend(self)
         backend.pointChanged.connect(self.onPointChanged)
+
         channel = QtWebChannel.QWebChannel(self)
         channel.registerObject('backend', backend)
+
         self.browser.page().setWebChannel(channel)
 
         # file = QtCore.QDir.current().absoluteFilePath("index.html")
         # map_view.load(QtCore.QUrl.fromLocalFile(file))
 
         x=[1, 2, 3]
         y=[4, 5, 6]
-        self.fig = go.FigureWidget([go.Scatter(x=x, y=y, mode='markers')])
+        self.fig : go.FigureWidget = go.FigureWidget([go.Scatter(x=x, y=y, mode='markers')])
 
-        scatter = self.fig.data[0]
+        # The data property is a tuple of the figure's trace objects
+        scatter = self.fig.data[0]  # FigureWidget
         scatter.on_click(self.update_point)
 
         self.browser.setHtml(self.fig.to_html(include_plotlyjs='cdn'))
@@ -81,6 +90,7 @@ def plot2(self):
 
     @out.capture(clear_output=True)
     def update_point(self, trace, points, selector):
+        sys.exit(1)
         print('!!!!')
 
     def show_graph(self):

sandbox/qt-plotly/utils.js

@@ -12,6 +12,7 @@ window.onload = function() {
         var mapDiv = 'map' + suffix;
         var map = API.map(mapDiv, {
             center: [51.505, -0.09],
+            // center: [38.575764, -121.478851],
             zoom: 4,
             dragging: true,
             scrollWheelZoom: true,
@@ -30,12 +31,14 @@ window.onload = function() {
             "name": "Grand Canyon USGS",
             "format": "png",
             "bounds": [15.976953506469728, 45.813157465613884],
+            // "bounds": [38.575764, -121.478851],
             "minzoom": 10,
             "version": "1.0.0",
             "maxzoom": 16,
             "center": [15.976953506469728,
                 45.813157465613884, 16
             ],
+            // "center": [38.575764, -121.478851],
             "type": "overlay",
             "description": "",
             "basename": "grandcanyon",

src/pymapmanager/interface2/mainMenus.py

@@ -425,6 +425,8 @@ def _refreshFileMenu(self):
 
         frontWindow = self.getApp().getFrontWindow()
 
+        logger.warning(f'frontWindow is:{frontWindow}')
+
         if isinstance(frontWindow, (mmWidget2, mapWidget)):
             if frontWindow.getPath().endswith('.mmap.zip'):
                 enableSave = False

src/pymapmanager/interface2/openFirstWindow.py

@@ -13,11 +13,12 @@
 from qtpy import QtCore, QtWidgets, QtGui
 
 import pymapmanager
-from pymapmanager.interface2.mainWindow import MainWindow
+# from pymapmanager.interface2.mainWindow import MainWindow
 
 from pymapmanager._logger import logger
 
-class OpenFirstWindow(MainWindow):
+# class OpenFirstWindow(MainWindow):
+class OpenFirstWindow(QtWidgets.QMainWindow):
     """A file/folder loading window.
     
     Open this at app start and close once a file/folder is loaded
@@ -29,6 +30,9 @@ def __init__(self,
 
         self._app : PyMapManagerApp = pyMapManagerApp
 
+        self.statusBar = QtWidgets.QStatusBar()
+        self.setStatusBar(self.statusBar)
+
         # self.recentStackList = self.getApp().getConfigDict().getRecentStacks()
         # self.recentMapList = self.getApp().getConfigDict().getRecentMaps()
 
@@ -53,8 +57,15 @@ def __init__(self,
 
         self.setWindowTitle('MapManager Open Files and Folders')
 
-    # def getApp(self):
-    #     return self._app
+    def setStatus(self, txt : str):
+        self.statusBar.showMessage(txt)
+
+    def getApp(self) -> "pymapmanager.interface2.PyMapManagerApp":
+        """Get running application.
+        """
+        # from PyQt5.QtWidgets import QApplication 
+        # return QApplication.instance()
+        return self._app
 
     # def _makeRecentTable(self, pathList : List[str], headerStr = ''):
     def _makeRecentTable(self, pathDictList : List[dict], headerStr = '') -> QtWidgets.QTableWidget:

src/pymapmanager/interface2/runInterfaceBob.py

@@ -27,17 +27,27 @@ def run():
     # path = '/Users/cudmore/Desktop/multi_timepoint_map_seg_spine_connected.mmap'
     # path = mapmanagercore.data.getMultiTimepointMap()
 
-    path = '/Users/cudmore/Desktop/olsen_example.mmap'
+    # path = '/Users/cudmore/Desktop/olsen_example.mmap'
+    path = '/Users/cudmore/Desktop/example_nd2.mmap'
+    path = '/Users/cudmore/Desktop/example_nd2.mmap.zip'
+    path = '/Users/cudmore/Sites/MapManagerCore-Data/data/Animal_145_Slice_1_Right.mmap.zip'
+    path = '/Users/cudmore/Desktop/Animal_145_Slice_1_Right.mmap.zip'
+
+    from mapmanagercore.data import getNd2Channel_1, getSingleTimepointMap_nd2
+    path = getNd2Channel_1()
+    path = getSingleTimepointMap_nd2()
 
     app = PyMapManagerApp(sys.argv)
     # mw will be map widget if path has multiple timepoints, otherwise mw is a stackwidget2
+
+    logger.info(f'loading stack widget from path:{path}')
     mw = app.loadStackWidget(path)
 
     # run a stack plugin
     # mw.runPlugin('Stack Contrast')
 
     # works
-    from pprint import pprint
+    # from pprint import pprint
     # logger.info('getTimeSeriesCore')
     # pprint(mw.getTimeSeriesCore().getMapImages().metadata(0).experimentMetadata.getValue('Species'))
     # pprint(mw.getTimeSeriesCore().getMapImages().metadata(0).experimentMetadata.asDict())

src/pymapmanager/timeseriesCore.py

@@ -144,16 +144,16 @@ def __init__(self, path : str):
 
         self._isDirty : bool = False
 
+        # when user drags/drops a mmap zarr DirectoryStore folder
+        if path.endswith('/'):
+            path = path[:-1]
+
         # TODO just use endswith(), splitext does not handle '.ome.zarr'
         _ext = os.path.splitext(path)[1]
-        # if path.endswith('.mmap') or path.endswith('.mmap/') or path.endswith('.mmap.zip'):
         if _ext in LOAD_SAVE_EXTENSIONS:
             self._load_zarr()
         elif path.endswith('.tif') or path.endswith('.nd2'):
             self._import_tiff()
-        # elif path.endswith('.ome.zarr'):
-        # elif path.endswith('.zarr') or path.endswith('.zarr/'):
-        #     self._import_ome_zarr()
         else:
             # TODO properly handle this
             logger.error(f'did not load file extension: "{_ext}"')