fix: correctly handles up and down clicked on auto-pilot ID

SchmollerLab · Jun 12, 2023 · 1609b69 · 1609b69
1 parent 2112d6e
commit 1609b69
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Showing 7 changed files with 272,393 additions and 281,662 deletions.
diff --git a/cellacdc/__main__.py b/cellacdc/__main__.py
@@ -1135,11 +1135,11 @@ def _showDataStructWin(self):
         txt = html_utils.paragraph(f"""
             Cell-ACDC can use the {bioformats_href} or the {aicsimageio_href}  
             libraries to read microscopy files.<br><br>
-            Bio-Formats requires Java and a python package called <code>javabridge</code>,<br>
+            <b>Bio-Formats requires Java</b> and a python package called <code>javabridge</code>,<br>
             that will be automatically installed if missing.<br><br>
             We recommend using Bio-Formats, since it can read the metadata of the file,<br> 
             such as pixel size, numerical aperture etc.<br><br>
-            If Bio-Formats fails, try using AICSImageIO.<br><br>
+            If <b>Bio-Formats fails, try using AICSImageIO</b>.<br><br>
             Alternatively, if you <b>already pre-processed your microsocpy files into .tif 
             files</b>,<br>
             you can choose to simply re-structure them into the Cell-ACDC compatible 
@@ -1149,15 +1149,15 @@ def _showDataStructWin(self):
             How do you want to proceed?          
         """)
         useAICSImageIO = QPushButton(
-            QIcon(':AICS_logo.png'), ' Use AICSImageIO ', msg
+            QIcon(':AICS_logo.svg'), ' Use AICSImageIO ', msg
         )
         useBioFormatsButton = QPushButton(
             QIcon(':ome.svg'), ' Use Bio-Formats ', msg
         )
         restructButton = QPushButton(
             QIcon(':folders.svg'), ' Re-structure image files ', msg
         )
-        _, useBioFormatsButton, restructButton = msg.question(
+        msg.question(
             self, 'How to structure files', txt, 
             buttonsTexts=(
                 'Cancel', useBioFormatsButton, useAICSImageIO, restructButton

diff --git a/cellacdc/apps.py b/cellacdc/apps.py
@@ -7427,6 +7427,8 @@ def __init__(self, expPaths: dict, infoPaths: dict=None, parent=None):
             for pos in positions:
                 if posFoldersInfo is not None:
                     status = posFoldersInfo.get(pos, '')
+                else:
+                    status = ''
                 pos_item_text = f'{pos}{status}'
                 pos_item = QTreeWidgetItem(exp_path_item, [pos_item_text])
                 pos_item.posFoldername = pos

diff --git a/cellacdc/gui.py b/cellacdc/gui.py
@@ -16599,11 +16599,13 @@ def addPointsByClickingButtonToggled(self, checked=True, sender=None):
         action.scatterItem.setVisible(True)
 
     def autoZoomNextObj(self):
+        self.sender().setValue(self.sender().value() - 1)
         self.pointsLayerAutoPilot('next')
         self.setFocusMain()
         self.setFocusGraphics()
 
     def autoZoomPrevObj(self):
+        self.sender().setValue(self.sender().value() + 1)
         self.pointsLayerAutoPilot('prev')
         self.setFocusMain()
         self.setFocusGraphics()

diff --git a/cellacdc/load.py b/cellacdc/load.py
@@ -1212,7 +1212,7 @@ def extractMetadata(self):
             self.PhysicalSizeZ = 1
 
         if 'LensNA' in self.metadata_df.index:
-            self.PhysicalSizeZ = float(
+            self.numAperture = float(
                 self.metadata_df.at['LensNA', 'values']
             )
         else: