ENH: Implement config generation from updated UI

TODO: decide and implement correct pairing of radiograph subfolders with
their camera calibration files

AutoscoperM/AutoscoperM.py

@@ -484,24 +484,29 @@ def onGenerateConfig(self):
         with slicer.util.tryWithErrorDisplay("Failed to compute results", waitCursor=True):
             volumeNode = self.ui.volumeSelector.currentNode()
             mainOutputDir = self.ui.mainOutputSelector.currentPath
-            trialName = self.ui.trialName.text
-            width = self.ui.vrgRes_width.value
-            height = self.ui.vrgRes_height.value
+            configFileName = self.ui.configFileName.text
+
+            configPath = os.path.join(mainOutputDir, f"{configFileName}.cfg")
 
             tiffSubDir = self.ui.tiffSubDir.text
             vrgSubDir = self.ui.vrgSubDir.text
             calibrationSubDir = self.ui.cameraSubDir.text
 
+            trialList = self.ui.trialList
+            partialVolumeList = self.ui.partialVolumeList
+            camCalList = self.ui.camCalList
+
             # Validate the inputs
             if not self.logic.validateInputs(
                 volumeNode=volumeNode,
                 mainOutputDir=mainOutputDir,
-                trialName=trialName,
-                width=width,
-                height=height,
-                volumeSubDir=tiffSubDir,
+                configFileName=configFileName,
+                tiffSubDir=tiffSubDir,
                 vrgSubDir=vrgSubDir,
                 calibrationSubDir=calibrationSubDir,
+                trialList=trialList,
+                partialVolumeList=partialVolumeList,
+                camCalList=camCalList,
             ):
                 raise ValueError("Invalid inputs")
                 return
@@ -514,6 +519,32 @@ def onGenerateConfig(self):
                 raise ValueError("Invalid paths")
                 return
 
+            def get_checked_items(listWidget):
+                checked_items = []
+                for idx in range(listWidget.count):
+                    item = listWidget.item(idx)
+                    if item.checkState() == qt.Qt.Checked:
+                        checked_items.append(item.text())
+                return checked_items
+
+            # extract filenames from UI lists, and use them to construct the paths relative to mainOutputDir
+            # FIXME: don't assume the list of camera files is given in the same order as list of radiograph root dir!
+            camCalFiles = [os.path.join(calibrationSubDir, item) for item in get_checked_items(camCalList)]
+            trialDirs = [os.path.join(vrgSubDir, item) for item in get_checked_items(trialList)]
+
+            if len(camCalFiles) != len(trialDirs):
+                raise ValueError(
+                    "Invalid inputs: number of selected trial directories must match the number "
+                    f"of camera calibration files: {len(camCalFiles)} != {len(trialDirs)}"
+                )
+                return
+
+            partialVolumeFiles = [os.path.join(tiffSubDir, item) for item in get_checked_items(partialVolumeList)]
+
+            if len(partialVolumeFiles) == 0:
+                raise ValueError("Invalid inputs: at least one volume file must be selected!")
+                return
+
             optimizationOffsets = [
                 self.ui.optOffX.value,
                 self.ui.optOffY.value,
@@ -529,24 +560,45 @@ def onGenerateConfig(self):
                 int(self.ui.flipZ.isChecked()),
             ]
 
+            renderResolution = [
+                self.ui.configRes_width.value,
+                self.ui.configRes_height.value,
+            ]
+
             voxel_spacing = [
                 self.ui.voxelSizeX.value,
                 self.ui.voxelSizeY.value,
                 self.ui.voxelSizeZ.value,
             ]
 
+            # Validate the inputs
+            if not self.logic.validateInputs(
+                *trialDirs,
+                *partialVolumeFiles,
+                *camCalFiles,
+                *optimizationOffsets,
+                *volumeFlip,
+                *renderResolution,
+                *voxel_spacing,
+            ):
+                raise ValueError("Invalid inputs")
+                return
+
             # generate the config file
-            configFilePath = IO.generateConfigFile(
-                mainOutputDir,
-                [tiffSubDir, vrgSubDir, calibrationSubDir],
-                trialName,
+            IO.generateConfigFile(
+                outputConfigPath=configPath,
+                trialName=configFileName,
+                camCalFiles=camCalFiles,
+                camRootDirs=trialDirs,
+                volumeFiles=partialVolumeFiles,
                 volumeFlip=volumeFlip,
                 voxelSize=voxel_spacing,
-                renderResolution=[int(width / 2), int(height / 2)],
+                renderResolution=renderResolution,
                 optimizationOffsets=optimizationOffsets,
             )
 
-            self.ui.configSelector.setCurrentPath(configFilePath)
+            # Set the path to this newly created config file in the "Config File" field in the Autoscoper Control UI
+            self.ui.configSelector.setCurrentPath(configPath)
         slicer.util.messageBox("Success!")
 
     def onImportModels(self):

AutoscoperM/AutoscoperMLib/IO.py

@@ -1,4 +1,3 @@
-import glob
 import logging
 import os
 from itertools import product
@@ -34,53 +33,34 @@ def loadSegmentation(segmentationNode: slicer.vtkMRMLSegmentationNode, filename:
 
 
 def generateConfigFile(
-    mainDirectory: str,
-    subDirectories: list[str],
+    outputConfigPath: str,
     trialName: str,
+    camCalFiles: list[str],
+    camRootDirs: list[str],
+    volumeFiles: list[str],
     volumeFlip: list[int],
     voxelSize: list[float],
     renderResolution: list[int],
     optimizationOffsets: list[float],
-) -> str:
+) -> None:
     """
     Generates the v1.1 config file for the trial
 
-    :param mainDirectory: Main directory
-    :param subDirectories: Sub directories
+    :param outputConfigPath: The absolute path to the config file to be generated
     :param trialName: Trial name
-    :param volumeFlip: Volume flip
-    :param voxelSize: Voxel size
-    :param renderResolution: Render resolution
-    :param optimizationOffsets: Optimization offsets
+    :param camCalFiles: The list of camera calibration file paths, relative to the main output dir
+    :param camRootDirs: The list of the radiograph directory paths, relative to the main output dir
+    :param volumeFiles: The list of tiff volume files, relative to the main output dir
+    :param volumeFlip: The flip settings for each of the volumes
+    :param voxelSize: The voxel size of each of the the volumes
+    :param renderResolution: The resolution of the 2D rendering of each of the volumes
+    :param optimizationOffsets: The offsets for the optimization
 
     :return: Path to the config file
     """
     import datetime
 
-    # Get the camera calibration files, camera root directories, and volumes
-    volumes = glob.glob(os.path.join(mainDirectory, subDirectories[0], "*.tif"))
-    cameraRootDirs = glob.glob(os.path.join(mainDirectory, subDirectories[1], "*"))
-    calibrationFiles = glob.glob(os.path.join(mainDirectory, subDirectories[2], "*.json"))
-
-    # Check that we have the same number of camera calibration files and camera root directories
-    if len(calibrationFiles) != len(cameraRootDirs):
-        logging.error(
-            "Number of camera calibration files and camera root directories do not match: "
-            " {len(calibrationFiles)} != {len(cameraRootDirs)}"
-        )
-        return None
-
-    # Check that we have at least one volume
-    if len(volumes) == 0:
-        logging.error("No volumes found!")
-        return None
-
-    # Transform the paths to be relative to the main directory
-    calibrationFiles = [os.path.relpath(calibrationFile, mainDirectory) for calibrationFile in calibrationFiles]
-    cameraRootDirs = [os.path.relpath(cameraRootDir, mainDirectory) for cameraRootDir in cameraRootDirs]
-    volumes = [os.path.relpath(volume, mainDirectory) for volume in volumes]
-
-    with open(os.path.join(mainDirectory, trialName + ".cfg"), "w+") as f:
+    with open(outputConfigPath, "w+") as f:
         # Trial Name as comment
         f.write(f"# {trialName} configuration file\n")
         f.write(
@@ -94,19 +74,19 @@ def generateConfigFile(
 
         # Camera Calibration Files
         f.write("# Camera Calibration Files\n")
-        for calibrationFile in calibrationFiles:
+        for calibrationFile in camCalFiles:
             f.write("mayaCam_csv " + calibrationFile + "\n")
         f.write("\n")
 
         # Camera Root Directories
         f.write("# Camera Root Directories\n")
-        for cameraRootDir in cameraRootDirs:
+        for cameraRootDir in camRootDirs:
             f.write("CameraRootDir " + cameraRootDir + "\n")
         f.write("\n")
 
         # Volumes
         f.write("# Volumes\n")
-        for volume in volumes:
+        for volume in volumeFiles:
             f.write("VolumeFile " + volume + "\n")
             f.write("VolumeFlip " + " ".join([str(x) for x in volumeFlip]) + "\n")
             f.write("VoxelSize " + " ".join([str(x) for x in voxelSize]) + "\n")
@@ -122,8 +102,6 @@ def generateConfigFile(
         f.write("OptimizationOffsets " + " ".join([str(x) for x in optimizationOffsets]) + "\n")
         f.write("\n")
 
-    return os.path.join(mainDirectory, trialName + ".cfg")
-
 
 def writeVolume(volumeNode: slicer.vtkMRMLVolumeNode, filename: str):
     """