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STYLE: Fix roiFromModelBounds style to streamline maintenance
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* Remove end of line spaces
* Reorder imports
* Prefer explicit imports instead of "*"
* Add missing spaces
* Add ARG002 linting exceptions for unused "modelBounds" parameters

Most of the fixes where either automatically fixed or identified
running `pre-commit run -a`.
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@jcfr @amymmorton
jcfr authored and amymmorton committed Dec 12, 2024
1 parent 38fed97 commit cdfcd23
Showing 1 changed file with 68 additions and 65 deletions.
133 changes: 68 additions & 65 deletions SVolModelROI/subVol_roi_model/roiFromModelBounds/roiFromModelBounds.py
View file
Original file line number Diff line number Diff line change
@@ -1,26 +1,23 @@
import glob
import logging
import os
from typing import Annotated, Optional

import pathlib
import vtk
import numpy as np
from typing import Optional

import numpy as np
import slicer
import vtk
from slicer import vtkMRMLMarkupsROINode, vtkMRMLModelNode, vtkMRMLScalarVolumeNode
from slicer.i18n import tr as _
from slicer.i18n import translate
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
from slicer.parameterNodeWrapper import (
parameterNodeWrapper,
WithinRange,
)

from slicer import vtkMRMLScalarVolumeNode
from slicer import vtkMRMLModelNode
from slicer import vtkMRMLMarkupsROINode

from slicer.ScriptedLoadableModule import (
ScriptedLoadableModule,
ScriptedLoadableModuleLogic,
ScriptedLoadableModuleTest,
ScriptedLoadableModuleWidget,
)
from slicer.util import VTKObservationMixin

#
# roiFromModelBounds
Expand All @@ -38,18 +35,22 @@ def __init__(self, parent):
# TODO: set categories (folders where the module shows up in the module selector)
self.parent.categories = ["Tracking"]
self.parent.dependencies = [] # TODO: add here list of module names that this module requires
self.parent.contributors = ["Amy Morton (Brown University)"]
self.parent.contributors = ["Amy Morton (Brown University)"]

# _() function marks text as translatable to other languages
self.parent.helpText = _("""
WIP modeule part of SlicerAutoscoperM
Intended to act as foundation fro subvolume 3d-3d volume registration
""")
self.parent.helpText = _(
"""
WIP module part of SlicerAutoscoperM
Intended to act as foundation for subvolume 3d-3d volume registration
"""
)
# TODO: replace with organization, grant and thanks
self.parent.acknowledgementText = _("""
self.parent.acknowledgementText = _(
"""
Template for this file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc., Andras Lasso, PerkLab,
and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
""")
"""
)

# Additional initialization step after application startup is complete
slicer.app.connect("startupCompleted()", registerSampleData)
Expand All @@ -63,7 +64,8 @@ def __init__(self, parent):
def registerSampleData():
"""Add data sets to Sample Data module."""
# It is always recommended to provide sample data for users to make it easy to try the module,
# but if no sample data is available then this method (and associated startupCompeted signal connection) can be removed.
# but if no sample data is available then this method (and associated startupCompeted signal
# connection) can be removed.

import SampleData

Expand All @@ -78,7 +80,8 @@ def registerSampleData():
category="roiFromModelBounds",
sampleName="roiFromModelBounds1",
# Thumbnail should have size of approximately 260x280 pixels and stored in Resources/Icons folder.
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images" set to "Single".
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images"
# set to "Single".
thumbnailFileName=os.path.join(iconsPath, "roiFromModelBounds1.png"),
# Download URL and target file name
uris="https://github.com/Slicer/SlicerTestingData/releases/download/SHA256/998cb522173839c78657f4bc0ea907cea09fd04e44601f17c82ea27927937b95",
Expand Down Expand Up @@ -121,6 +124,7 @@ class roiFromModelBoundsParameterNode:
modelROI - The output volume that will contain the thresholded volume.
croppedVolume - The output volume that will be .
"""

modelFile_path: pathlib.Path
inputVolume: vtkMRMLScalarVolumeNode
modelBounds: float
Expand Down Expand Up @@ -172,7 +176,7 @@ def setup(self) -> None:
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent, self.onSceneEndClose)

# Buttons
#self.ui.applyButton.connect("clicked(bool)", self.onApplyButton)
# self.ui.applyButton.connect("clicked(bool)", self.onApplyButton)
self.ui.showBounds_pb.connect("clicked(bool)", self.onShowModelBoundsButton)

# Make sure parameter node is initialized (needed for module reload)
Expand All @@ -195,12 +199,12 @@ def exit(self) -> None:
self._parameterNodeGuiTag = None
self.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self._checkCanGenModelROI)

def onSceneStartClose(self, caller, event) -> None:
def onSceneStartClose(self, _caller, _event) -> None:
"""Called just before the scene is closed."""
# Parameter node will be reset, do not use it anymore
self.setParameterNode(None)

def onSceneEndClose(self, caller, event) -> None:
def onSceneEndClose(self, _caller, _event) -> None:
"""Called just after the scene is closed."""
# If this module is shown while the scene is closed then recreate a new parameter node immediately
if self.parent.isEntered:
Expand All @@ -214,12 +218,12 @@ def initializeParameterNode(self) -> None:
self.setParameterNode(self.logic.getParameterNode())

# Select default input nodes if nothing is selected yet to save a few clicks for the user
#if not self._parameterNode.inputModel:
# if not self._parameterNode.inputModel:
# firstModelNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLModelNode")
# if firstModelNode:
# self._parameterNode.inputModel = firstModelNode

#if not self._parameterNode.inputVolume:
# if not self._parameterNode.inputVolume:
# firstVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
# if firstVolumeNode:
# self._parameterNode.inputVolume = firstVolumeNode
Expand All @@ -241,36 +245,35 @@ def setParameterNode(self, inputParameterNode: Optional[roiFromModelBoundsParame
self.addObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self._checkCanGenModelROI)
self._checkCanGenModelROI()

def _checkCanGenModelROI(self, caller=None, event=None) -> None:
def _checkCanGenModelROI(self, _caller=None, _event=None) -> None:
if self._parameterNode and self._parameterNode.inputVolume and self._parameterNode.modelFile_path:
self.ui.showBounds_pb.toolTip = _("Compute output volume")
self.ui.showBounds_pb.enabled = True
else:
self.ui.showBounds_pb.toolTip = _("Select input ModelPath and volume nodes")
self.ui.showBounds_pb.enabled = True


def onShowModelBoundsButton(self) -> None:
with slicer.util.tryWithErrorDisplay(_("Failed to compute results."), waitCursor=True):
# Compute output
volumeNode = self.ui.inputVolSelector.currentNode()
modelFileDir = self.ui.modelPath_lineEdit.currentPath
#TO DO write validatePaths logic funciton

# TO DO write validatePaths logic function
# if not self.logic.validatePaths(modelFileDir=modelFileDir):
# raise ValueError("Invalid paths")
# return
modelFiles = glob.glob(os.path.join(modelFileDir, "*.*"))
for indx, file in enumerate(modelFiles):

for _indx, file in enumerate(modelFiles):
modelNode = slicer.util.loadNodeFromFile(file)
modelNode.CreateDefaultDisplayNodes()
self.logic.modelBounds(modelNode,volumeNode,
self.ui.modelROISelector, self.ui.cropVolSelector)

#self.logic.modelBounds(self.ui.inputSelector.currentNode(),self.ui.inputVolumeSelector,
self.logic.modelBounds(modelNode, volumeNode, self.ui.modelROISelector, self.ui.cropVolSelector)

# self.logic.modelBounds(self.ui.inputSelector.currentNode(),self.ui.inputVolumeSelector,
# self.ui.modelROISelector, self.ui.cropVolSelector)


#
# roiFromModelBoundsLogic
#
Expand All @@ -293,46 +296,46 @@ def __init__(self) -> None:
def getParameterNode(self):
return roiFromModelBoundsParameterNode(super().getParameterNode())

def modelBounds(self,
inputModel:vtkMRMLModelNode,
inputVolume: vtkMRMLScalarVolumeNode,
modelROI: vtkMRMLMarkupsROINode,
croppedVolume: vtkMRMLScalarVolumeNode) -> None:
def modelBounds(
self,
inputModel: vtkMRMLModelNode,
inputVolume: vtkMRMLScalarVolumeNode, # noqa: ARG002
modelROI: vtkMRMLMarkupsROINode,
croppedVolume: vtkMRMLScalarVolumeNode, # noqa: ARG002
) -> None:

tB = [0.0,0.0,0.0,0.0,0.0,0.0]
tB = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
inputModel.GetBounds(tB)
#print(tB)
#modelC = [0.0]*3
#modelSize = [0.0]*3
#strange that the model nodes have a getBounds- but no center and size..
#and the roi has bno.. set Bounds- just center and size
# print(tB)
# modelC = [0.0]*3
# modelSize = [0.0]*3
# strange that the model nodes have a getBounds- but no center and size..
# and the roi has bno.. set Bounds- just center and size

#numpy for array operatots:
tnp_min = np.array([tB[0],tB[2],tB[4]])
tnp_max = np.array([tB[1],tB[3],tB[5]])
# numpy for array operatots:
tnp_min = np.array([tB[0], tB[2], tB[4]])
tnp_max = np.array([tB[1], tB[3], tB[5]])

tnp_C = (tnp_min+tnp_max)/2
tnpS = (tnp_min-tnp_max)
tnp_C = (tnp_min + tnp_max) / 2
tnpS = tnp_min - tnp_max

#inputModel.GetCenter(modelC)
#inputModel.GetSize(modelSize)
# inputModel.GetCenter(modelC)
# inputModel.GetSize(modelSize)
mname = inputModel.GetName()

#use tB lims to size roi
#Create ROI node
modelROI = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode")
# use tB lims to size roi
# Create ROI node
modelROI = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode")
modelROI.SetCenter(tnp_C.tolist())
modelROI.SetSize(tnpS.tolist())
modelROI.CreateDefaultDisplayNodes() # only needed for display

roi_name =mname+"_roi"
roi_name = mname + "_roi"
modelROI.SetName(roi_name)

#populate in Model ROI Output..?

#print(modelROI)

# populate in Model ROI Output..?

# print(modelROI)


#
Expand Down

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