diff --git a/AutoscoperM/AutoscoperM.py b/AutoscoperM/AutoscoperM.py
index 1a42746..0db2a12 100644
--- a/AutoscoperM/AutoscoperM.py
+++ b/AutoscoperM/AutoscoperM.py
@@ -18,7 +18,7 @@
)
from slicer.util import VTKObservationMixin
-from AutoscoperMLib import IO, SubVolumeExtraction
+from AutoscoperMLib import IO, SubVolumeExtraction, Validation
#
# AutoscoperM
@@ -447,7 +447,8 @@ def onGeneratePartialVolumes(self):
trackingSubDir = self.ui.trackingSubDir.text
modelSubDir = self.ui.modelSubDir.text
segmentationNode = self.ui.pv_SegNodeComboBox.currentNode()
- if not self.logic.validateInputs(
+
+ Validation.validateInputs(
volumeNode=volumeNode,
segmentationNode=segmentationNode,
mainOutputDir=mainOutputDir,
@@ -455,9 +456,7 @@ def onGeneratePartialVolumes(self):
transformSubDir=tfmSubDir,
trackingSubDir=trackingSubDir,
modelSubDir=modelSubDir,
- ):
- raise ValueError("Invalid inputs")
- return
+ )
self.logic.createPathsIfNotExists(
mainOutputDir,
@@ -503,7 +502,7 @@ def onGenerateConfig(self):
camCalList = self.ui.camCalList
# Validate the inputs
- if not self.logic.validateInputs(
+ Validation.validateInputs(
volumeNode=volumeNode,
mainOutputDir=mainOutputDir,
configFileName=configFileName,
@@ -513,17 +512,13 @@ def onGenerateConfig(self):
trialList=trialList,
partialVolumeList=partialVolumeList,
camCalList=camCalList,
- ):
- raise ValueError("Invalid inputs")
- return
- if not self.logic.validatePaths(
+ )
+ Validation.validatePaths(
mainOutputDir=mainOutputDir,
tiffDir=os.path.join(mainOutputDir, tiffSubDir),
radiographSubDir=os.path.join(mainOutputDir, radiographSubDir),
calibDir=os.path.join(mainOutputDir, calibrationSubDir),
- ):
- raise ValueError("Invalid paths")
- return
+ )
def get_staged_items(listWidget):
staged_items = []
@@ -600,8 +595,8 @@ def get_checked_items(listWidget):
self.ui.voxelSizeZ.value,
]
- # Validate the inputs
- if not self.logic.validateInputs(
+ # Validate the extracted parameters
+ Validation.validateInputs(
*trialDirs,
*partialVolumeFiles,
*camCalFiles,
@@ -609,8 +604,7 @@ def get_checked_items(listWidget):
*volumeFlip,
*renderResolution,
*voxel_spacing,
- ):
- raise ValueError("Invalid inputs")
+ )
# generate the config file
IO.generateConfigFile(
@@ -639,15 +633,13 @@ def onImportModels(self):
volumeNode = self.ui.volumeSelector.currentNode()
- if not self.logic.validateInputs(voluemNode=volumeNode):
- raise ValueError("Invalid inputs")
- return
+ Validation.validateInputs(volumeNode=volumeNode)
if self.ui.segSTL_loadRadioButton.isChecked():
segmentationFileDir = self.ui.segSTL_modelsDir.currentPath
- if not self.logic.validatePaths(segmentationFileDir=segmentationFileDir):
- raise ValueError("Invalid paths")
- return
+
+ Validation.validatePaths(segmentationFileDir=segmentationFileDir)
+
segmentationFiles = glob.glob(os.path.join(segmentationFileDir, "*.*"))
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes()
@@ -660,7 +652,7 @@ def onImportModels(self):
slicer.mrmlScene.RemoveNode(returnedNode)
self.ui.progressBar.setValue((idx + 1) / len(segmentationFiles) * 100)
else: # Should never happen but just in case
- raise Exception("Please select the 'Segmentation From Model' option in order to import models")
+ raise ValueError("Please select the 'Segmentation From Model' option in order to import models")
return
slicer.util.messageBox("Success!")
@@ -674,9 +666,7 @@ def onSegmentation(self):
volumeNode = self.ui.volumeSelector.currentNode()
- if not self.logic.validateInputs(voluemNode=volumeNode):
- raise ValueError("Invalid inputs")
- return
+ Validation.validateInputs(volumeNode=volumeNode)
if self.ui.segGen_autoRadioButton.isChecked():
currentVolumeNode = volumeNode
@@ -702,7 +692,7 @@ def onSegmentation(self):
slicer.mrmlScene.RemoveNode(segmentationNode)
currentVolumeNode = self.logic.getNextItemInSequence(volumeNode)
else: # Should never happen but just in case
- raise Exception("Please select the 'Automatic Segmentation' option in order to generate segmentations")
+ raise ValueError("Please select the 'Automatic Segmentation' option in order to generate segmentations")
return
slicer.util.messageBox("Success!")
@@ -725,7 +715,7 @@ def onLoadPV(self):
tfms_scale = glob.glob(os.path.join(mainOutputDir, transformSubDir, "*_scale.tfm"))
if len(vols) == 0:
- raise Exception("No data found")
+ raise ValueError("No data found")
return
if len(vols) != len(tfms_t) != len(tfms_scale):
@@ -801,18 +791,14 @@ def populateListFromOutputSubDir(self, listWidget, fileSubDir, itemType="file"):
listWidget.clear()
mainOutputDir = self.ui.mainOutputSelector.currentPath
- if not self.logic.validateInputs(
+ Validation.validateInputs(
listWidget=listWidget,
mainOutputDir=mainOutputDir,
fileSubDir=fileSubDir,
- ):
- raise ValueError("Invalid inputs")
- return
+ )
fileDir = os.path.join(mainOutputDir, fileSubDir)
- if not self.logic.validatePaths(fileDir=fileDir):
- raise ValueError(f"Invalid input: subdirectory '{fileDir}' does not exist.")
- return
+ Validation.validatePaths(fileDir=fileDir)
if itemType == "file":
listFiles = [f.name for f in os.scandir(fileDir) if os.path.isfile(f)]
@@ -1181,66 +1167,6 @@ def showVolumeIn3D(volumeNode: slicer.vtkMRMLVolumeNode):
logic.UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode)
slicer.mrmlScene.RemoveNode(slicer.util.getNode("Volume rendering ROI"))
- @staticmethod
- def validateInputs(*args: tuple, **kwargs: dict) -> bool:
- """
- Validates that the provided inputs are not None.
-
- :param args: list of inputs to validate
- :param kwargs: list of inputs to validate
-
- :return: True if all inputs are valid, False otherwise
- """
- statuses = []
- for arg in args:
- status = True
- if arg is None:
- logging.error(f"{arg} is None")
- status = False
- if isinstance(arg, str) and arg == "":
- logging.error(f"{arg} is an empty string")
- status = False
- statuses.append(status)
-
- for name, arg in kwargs.items():
- status = True
- if arg is None:
- logging.error(f"{name} is None")
- status = False
- if isinstance(arg, str) and arg == "":
- logging.error(f"{name} is an empty string")
- status = False
- statuses.append(status)
-
- return all(statuses)
-
- @staticmethod
- def validatePaths(*args: tuple, **kwargs: dict) -> bool:
- """
- Checks that the provided paths exist.
-
- :param args: list of paths to validate
- :param kwargs: list of paths to validate
-
- :return: True if all paths exist, False otherwise
- """
- statuses = []
- for arg in args:
- status = True
- if not os.path.exists(arg):
- logging.error(f"{arg} does not exist")
- status = False
- statuses.append(status)
-
- for name, path in kwargs.items():
- status = True
- if not os.path.exists(path):
- logging.error(f"{name} ({path}) does not exist")
- status = False
- statuses.append(status)
-
- return all(statuses)
-
@staticmethod
def createPathsIfNotExists(*args: tuple) -> None:
"""
diff --git a/AutoscoperM/AutoscoperMLib/Validation.py b/AutoscoperM/AutoscoperMLib/Validation.py
new file mode 100644
index 0000000..1de2a35
--- /dev/null
+++ b/AutoscoperM/AutoscoperMLib/Validation.py
@@ -0,0 +1,64 @@
+import os
+
+
+class ValueErrorsException(Exception):
+ """A custom exception class that accepts a list of errors."""
+
+ def __init__(self, errors):
+ if not isinstance(errors, list):
+ raise ValueError("The errors input must be a list")
+ if len(errors) < 1:
+ raise ValueError("The errors list must contain at least one error")
+ self.errors = errors
+ super().__init__("\n".join(errors))
+
+ def __str__(self):
+ err_str = "Invalid value{}".format("" if len(self.errors) == 0 else "s")
+
+ return err_str + ":\n" + "\n".join(self.errors)
+
+
+def validateInputs(*args: tuple, **kwargs: dict) -> None:
+ """
+ Validates that the provided inputs are not None or empty.
+
+ :param args: list of inputs to validate
+ :param kwargs: dictionary of inputs to validate
+ :raises: ValueErrorsException
+ """
+ errors = []
+ for arg in args:
+ if arg is None:
+ errors.append("Input argument is None")
+ if isinstance(arg, str) and arg == "":
+ errors.append("Input argument is an empty string")
+
+ for name, arg in kwargs.items():
+ if arg is None:
+ errors.append(f"Input '{name}' is None")
+ if isinstance(arg, str) and arg == "":
+ errors.append(f"Input '{name}' is an empty string")
+
+ if len(errors) > 0:
+ raise ValueErrorsException(errors)
+
+
+def validatePaths(*args: tuple, **kwargs: dict) -> None:
+ """
+ Checks that the provided paths exist.
+
+ :param args: list of paths to validate
+ :param kwargs: list of paths to validate
+ :raises: ValueErrorsException
+ """
+ errors = []
+ for arg in args:
+ if not os.path.exists(arg):
+ errors.append(f"Input path '{arg}' does not exist")
+
+ for name, path in kwargs.items():
+ if not os.path.exists(path):
+ errors.append(f"Input path '{name}' ({path}) does not exist")
+
+ if len(errors) > 0:
+ raise ValueErrorsException(errors)
diff --git a/AutoscoperM/CMakeLists.txt b/AutoscoperM/CMakeLists.txt
index f752650..f84983a 100644
--- a/AutoscoperM/CMakeLists.txt
+++ b/AutoscoperM/CMakeLists.txt
@@ -7,6 +7,7 @@ set(MODULE_PYTHON_SCRIPTS
${MODULE_NAME}Lib/__init__.py
${MODULE_NAME}Lib/IO.py
${MODULE_NAME}Lib/SubVolumeExtraction.py
+ ${MODULE_NAME}Lib/Validation.py
)
set(MODULE_PYTHON_RESOURCES