Fix trailing whitespace and basic formatting issues

Co-authored-by: beniroquai <[email protected]>

Author: Copilot

imswitch/__init__.py

@@ -7,8 +7,8 @@
 jupyternotebookurl = ""
 __argparse__ = None
 
-''' 
-These are flags to ensure headless operation and side-loading of the config file 
+'''
+These are flags to ensure headless operation and side-loading of the config file
 '''
 IS_HEADLESS = False
 DEFAULT_SETUP_FILE = None

imswitch/__main__.py

@@ -9,17 +9,17 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
          data_folder: str=None, scan_ext_data_folder:bool=None, ext_drive_mount:str=None):
     '''
     is_headless: bool => start with or without qt
-    default_config: str => path to the config file 
+    default_config: str => path to the config file
     http_port: int => port number (default: 8001)
     socket_port: int => port number (default: 8002)
     ssl: bool => use ssl (default: True)
     config_folder: str => path to the config folder (default: None, pointing to Documents/ImSwitch)
     data_folder: str => path to the data folder (default: None, pointing to Documents/ImSwitchConfig)
     scan_ext_data_folder: bool => if True, we will scan the ext_drive_mount for usb drives and use this for data storage
     ext_drive_mount: str => path to the external drive mount point (default: None, optionally pointing to e.g. /Volumes or /media)
-    
-    
-    
+
+
+
     To start imswitch in headless using the arguments, you can call the main file with the following arguments:
         python main.py --headless or
         python -m imswitch --headless 1 --config-file example_virtual_microscope.json --config-folder /Users/bene/Downloads --scan-ext-drive-mount true --ext-data-folder ~/Downloads --ext-drive-mount /Volumes
@@ -40,37 +40,37 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
             parser.add_argument('--http-port', dest='http_port', type=int, default=8001,
                                 help='specify http port')
 
-            # specify socket port 
+            # specify socket port
             parser.add_argument('--socket-port', dest='socket_port', type=int, default=8002,
                                 help='specify socket port')
             # specify ssl
             parser.add_argument('--no-ssl', dest='ssl', default=True, action='store_false',
                                 help='specify ssl')
-            
+
             # specify the config folder (e.g. if running from a different location / container)
             parser.add_argument('--config-folder', dest='config_folder', type=str, default=None,
                                 help='specify config folder')
-            
-            parser.add_argument('--ext-data-folder', dest='data_folder', type=str, default=None, 
+
+            parser.add_argument('--ext-data-folder', dest='data_folder', type=str, default=None,
                                 help='point to a folder to store the data. This is the default location for the data folder. If not specified, the default location will be used.')
 
             parser.add_argument('--scan-ext-drive-mount', dest='scan_ext_data_folder', default=False, action='store_true',
                                 help='scan the external mount (linux only) if we have a USB drive to save to')
-            
+
             parser.add_argument('--ext-drive-mount', dest='ext_drive_mount', type=str, default=None,
                                 help='specify the external drive mount point (e.g. /Volumes or /media)')
-            
-            
-            
+
+
+
             args = parser.parse_args()
-            
-            imswitch.IS_HEADLESS = args.headless            # if True, no QT will be loaded   
+
+            imswitch.IS_HEADLESS = args.headless            # if True, no QT will be loaded
             imswitch.__httpport__ = args.http_port          # e.g. 8001
             imswitch.__ssl__ = args.ssl                     # if True, ssl will be used (e.g. https)
             imswitch.__socketport__ = args.socket_port      # e.g. 8002
-            
+
             if type(args.config_file)==str and args.config_file.find("json")>=0:  # e.g. example_virtual_microscope.json
-                imswitch.DEFAULT_SETUP_FILE = args.config_file  
+                imswitch.DEFAULT_SETUP_FILE = args.config_file
             if args.config_folder and os.path.isdir(args.config_folder):
                 imswitch.DEFAULT_CONFIG_PATH = args.config_folder # e.g. /Users/USER/ in case an alternative path is used
             if args.data_folder and os.path.isdir(args.data_folder):
@@ -79,7 +79,7 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
                 imswitch.SCAN_EXT_DATA_FOLDER = args.scan_ext_data_folder
             if args.ext_drive_mount:
                 imswitch.EXT_DRIVE_MOUNT = args.ext_drive_mount
-            
+
         except Exception as e:
             print(e)
             pass
@@ -123,7 +123,7 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
         logger.info(f'Config file: {imswitch.DEFAULT_SETUP_FILE}')
         logger.info(f'Config folder: {imswitch.DEFAULT_CONFIG_PATH}')
         logger.info(f'Data folder: {imswitch.DEFAULT_DATA_PATH}')
-        
+
         if imswitch.IS_HEADLESS:
             app = None
         else:
@@ -151,7 +151,7 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
         # connect the different controllers through the communication channel
         moduleCommChannel = ModuleCommunicationChannel()
 
-        # only create the GUI if necessary 
+        # only create the GUI if necessary
         if not imswitch.IS_HEADLESS:
             from imswitch.imcommon.view import MultiModuleWindow, ModuleLoadErrorView
             multiModuleWindow = MultiModuleWindow('ImSwitch')
@@ -178,15 +178,15 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
             # The displayed module name will be the module's __title__, or alternatively its ID if
             # __title__ is not set
             moduleName = modulePkg.__title__ if hasattr(modulePkg, '__title__') else moduleId
-            # we load all the controllers, managers and widgets here: 
+            # we load all the controllers, managers and widgets here:
             try:
                 view, controller = modulePkg.getMainViewAndController(
                     moduleCommChannel=moduleCommChannel,
                     multiModuleWindowController=multiModuleWindowController,
                     moduleMainControllers=moduleMainControllers
                 )
                 logger.info(f'initialize module {moduleId}')
-                
+
             except Exception as e:
                 logger.error(f'Failed to initialize module {moduleId}')
                 logger.error(e)
@@ -197,11 +197,11 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, soc
                     multiModuleWindow.addModule(moduleId, moduleName, ModuleLoadErrorView(e))
             else:
                 # Add module to window
-                if not imswitch.IS_HEADLESS: 
+                if not imswitch.IS_HEADLESS:
                     multiModuleWindow.addModule(moduleId, moduleName, view)
                 moduleMainControllers[moduleId] = controller
-                
-                # in case of the imnotebook, spread the notebook url 
+
+                # in case of the imnotebook, spread the notebook url
                 if moduleId == 'imnotebook':
                     imswitch.jupyternotebookurl = controller.webaddr
 

imswitch/_data/images/calculatewellplatepositions.py

@@ -1,12 +1,12 @@
-#%% compute the positions of wells in a wellplate 
+#%% compute the positions of wells in a wellplate
 
-import json 
+import json
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
 
 #%%
-# read in the json file with the coordinates 
+# read in the json file with the coordinates
 pixelsize_eff = .31 # um from camera
 overlap = 0.75 # 25% overlap
 n_pix_x, n_pix_y = 4000,3000
@@ -29,7 +29,7 @@
     n_tiles_x = int(2*radius/fov_physical_x) # number of pixels in the radius
     n_tiles_y = int(2*radius/fov_physical_y) # number of pixels in the radius
 
-    # % create xx/yy meshgrid 
+    # % create xx/yy meshgrid
     xx,yy = np.meshgrid(fov_physical_x*np.arange(-n_tiles_x//2,n_tiles_x//2)+1,fov_physical_y*np.arange(-n_tiles_y//2,n_tiles_y//2)+1)
     circle = ((xx)**2+(yy)**2) < radius**2
 
@@ -44,7 +44,7 @@
 
     for well in data['ScanParameters']['wells']:
         center_x, center_y = well['positionX'], well['positionY']
-        
+
         if 0:
             plt.plot(well_scan_locations[0]+center_x,well_scan_locations[1]+center_y,'r.')
             plt.plot(center_x,center_y,'b.')
@@ -54,10 +54,10 @@
                 plt.gca().add_patch(rect)
     plt.show()
 
-        
 
 
-        
+
+
 # %%
 
 # %%

imswitch/_data/images/samplelayouts/generateWellplateJSON.py

@@ -1,5 +1,5 @@
 import json
-import os 
+import os
 
 def generate_wellplate_json(
     name,
@@ -30,11 +30,11 @@ def generate_wellplate_json(
             wells.append({
                 "wellID": f"{chr(65+j)}{i+1}",
                 "positionX": well_x,
-                "positionY": well_y, 
+                "positionY": well_y,
                 "positionXpx": well_x * pixel_image_x / phys_dim_x,
                 "positionYpx": well_y * pixel_image_y / phys_dim_y,
-                "idX": i, 
-                "idY": j, 
+                "idX": i,
+                "idY": j,
                 "idN": idN,
                 "positionXmin": well_x - well_radius,
                 "positionXmax": well_x + well_radius,
@@ -62,9 +62,9 @@ def generate_wellplate_json(
     return data
 
 imageFilePaths = [
-                  'images/samplelayouts/6wellplate_1509x1010.png', 
-                  'images/samplelayouts/12wellplate_1509x1010.png', 
-                  'images/samplelayouts/24wellplate_1509x1010.png', 
+                  'images/samplelayouts/6wellplate_1509x1010.png',
+                  'images/samplelayouts/12wellplate_1509x1010.png',
+                  'images/samplelayouts/24wellplate_1509x1010.png',
                   'images/samplelayouts/96wellplate_1509x1010.png']
 
 parameterPerImage = [
@@ -81,7 +81,7 @@ def generate_wellplate_json(
         "center_x": 63.85,
         "center_y": 42.75,
         "well_spacing_x": 31,
-        "well_spacing_y": 0, 
+        "well_spacing_y": 0,
         "well_radius": 10,
         "filePath": 'images/samplelayouts/4slidecarrier_1509x1010.png'
     },
@@ -98,7 +98,7 @@ def generate_wellplate_json(
         "center_x": 63.85,
         "center_y": 42.75,
         "well_spacing_x": 39,
-        "well_spacing_y": 39, 
+        "well_spacing_y": 39,
         "well_radius": 17.5,
         "filePath": 'images/samplelayouts/6wellplate_1509x1010.png'
     },
@@ -133,7 +133,7 @@ def generate_wellplate_json(
         "center_y": 42.75,
         "well_spacing_x": 18.9,
         "well_spacing_y": 18.9,
-        "well_radius": 6.5,  
+        "well_radius": 6.5,
         "filePath": 'images/samplelayouts/24wellplate_1509x1010.png'
     },
     {
@@ -156,7 +156,7 @@ def generate_wellplate_json(
 ]
 
 for iWellplate in parameterPerImage:
-    
+
     wellplate_json = generate_wellplate_json(
         name = iWellplate['name'],
         pixel_image_x = iWellplate['pixel_image_x'],
@@ -175,7 +175,7 @@ def generate_wellplate_json(
         well_radius = iWellplate['well_radius']
     )
     basePath = 'imswitch/_data/images/'
-    
+
     json_file_path = os.path.join(basePath, f"{iWellplate['name'].replace(' ', '_').lower()}.json")
 
     with open(json_file_path, "w") as file:

imswitch/_data/user_defaults/scripts/lightsheet_psf_ac.py

@@ -33,14 +33,14 @@
 for i in range(num_steps):
     # Relative move, step size 5
     api.imcontrol.movePositioner(positionerName, "X", step_size, False, True)
-    
+
     # Wait 50ms before proceeding
     time.sleep(1)
-    
+
     # Capture image
     image = api.imcontrol.snapImage(True, False)
     mImageList.append(image)
-    
+
     # Optional: Print current position
     current_position = start_X + (i + 1) * step_size
     print(f"Image captured at position X = {current_position}.")

imswitch/_data/user_defaults/scripts/uc2_move_positoinlist.py

@@ -58,7 +58,7 @@
 	for iy in range(2):
 		mPos = (ix*xDim*mOverlap+58000,
 		 iy*yDim*mOverlap+23000)
-		
+
 		api.imcontrol.movePositioner(positionerName, "XY", mPos, True, True)
 		time.sleep(0.5)
 		# api.imcontrol.snapImageToPath(str(ix)+"_"+str(iy))
@@ -97,7 +97,7 @@
     #iPos = 0
     #for position in positions:
     #    posX, posY, posZ = position
-        
+
     #    api.imcontrol.movePositioner(positionerName, "X", posX, True, True)
     #    api.imcontrol.movePositioner(positionerName, "Y", posY, True, True)
     #    api.imcontrol.movePositioner(positionerName, "Z", posZ, True, True)

imswitch/imcommon/applaunch.py

@@ -8,7 +8,7 @@
 from ipykernel.embed import embed_kernel   # pip install ipykernel
 
 from .model import dirtools, pythontools, initLogger
-from imswitch.imcommon.framework import Signal, Thread     
+from imswitch.imcommon.framework import Signal, Thread
 from imswitch import IS_HEADLESS
 if not IS_HEADLESS:
     from qtpy import QtCore, QtGui, QtWidgets
@@ -49,7 +49,7 @@ def prepareApp():
     QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_DisableHighDpiScaling, True) # proper scaling on Mac?
     #QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps, True)
     # https://stackoverflow.com/questions/72131093/pyqt5-qwebengineview-doesnt-load-url
-    # The following element (sandbox) is to keep the app from crashing when using QWebEngineView    
+    # The following element (sandbox) is to keep the app from crashing when using QWebEngineView
     app = QtWidgets.QApplication(['', '--no-sandbox'])
     app.setWindowIcon(QtGui.QIcon(os.path.join(dirtools.DataFileDirs.Root, 'icon.png')))
     app.setStyleSheet(getBaseStyleSheet())
@@ -64,7 +64,7 @@ def launchApp(app, mainView, moduleMainControllers):
     if IS_HEADLESS:
         """We won't have any GUI, so we don't need to prepare the app."""
         # Keep python running
-        # embed_kernel() # TODO: This should be non-blocking! 
+        # embed_kernel() # TODO: This should be non-blocking!
         tDiskCheck = time.time()
         while True: # TODO: have webserver signal somehow?
             try:
@@ -74,11 +74,11 @@ def launchApp(app, mainView, moduleMainControllers):
                     # if the storage is full or the user presses Ctrl+C, we want to stop the experiment
                     moduleMainControllers.mapping["imcontrol"]._ImConMainController__commChannel.sigExperimentStop.emit()
                     tDiskCheck = time.time()
-                    
+
             except KeyboardInterrupt:
                 exitCode = 0
                 break
-        
+
     else:
         # Show app
         if mainView is not None:

imswitch/imcommon/controller/CheckUpdatesController.py

@@ -10,7 +10,7 @@
 import datetime
 
 from imswitch import IS_HEADLESS, __version__
-from imswitch.imcommon.framework import Signal, Thread 
+from imswitch.imcommon.framework import Signal, Thread
 from imswitch.imcommon.model import initLogger
 from .basecontrollers import WidgetController
 
@@ -72,7 +72,7 @@ def run(self):
                     ## attempting to downloda the current ImSwitch version
                     downloadURL = releaseResponse.json()['assets'][0]['browser_download_url']
                     self.__logger.debug("We are downloading the software from: "+downloadURL)
-                
+
                     ## inplace replacement won't work I guess? => seems to work
                     def dlImSwitch(downloadURL, fileName):
                         resultDL = urllib.request.urlretrieve(downloadURL, fileName)
@@ -84,7 +84,7 @@ def dlImSwitch(downloadURL, fileName):
                     mThread.join()
 
                     # make a backup copy of the file
-                    if os.path.isfile(ImSwitchExeFilename):                    
+                    if os.path.isfile(ImSwitchExeFilename):
                         self.__logger.debug("Renaming old ImSwitch.exe file")
                         tz = datetime.timezone.utc
                         ft = "%Y-%m-%dT%H-%M-%S"
@@ -97,8 +97,8 @@ def dlImSwitch(downloadURL, fileName):
                     self.__logger.debug("Download successful!")
                     self.sigNewVersionShowInfo.emit("Download successful! Please restart ImSwitch. ")
 
-                    
-                
+
+
                 else:
                     self.sigNoUpdate.emit()
             else:
@@ -117,8 +117,8 @@ def dlImSwitch(downloadURL, fileName):
             #self.sigFailed.emit()
             self.sigNewVersionShowInfo.emit("Updating failed. "+str(e))
 
-            
-            
+
+
     def getCurrentCommitDate(self):
         return str(subprocess.check_output(['git', 'log', '-n', '1', '--pretty=tformat:%h-%ad', '--date=short']).strip()).split("-")[-3:]