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4DCT / Sequential 3DCT #75

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merged 10 commits into from
Apr 18, 2024
Merged

4DCT / Sequential 3DCT #75

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caa19cd
ENH: Expand Piplines to Sequential 3D and 4DCT
NicerNewerCar Oct 6, 2023
687f51b
BUG: Fix config generation
NicerNewerCar Mar 11, 2024
8f573f7
ENH: Update radiograph file names
NicerNewerCar Mar 11, 2024
7e588b9
ENH: Speed up VRG and DID
NicerNewerCar Mar 18, 2024
7f4eb0e
ENH: Ensure RAS to LPS flips are enabled by default
NicerNewerCar Mar 18, 2024
27eb11a
DOC: Remove redundant sphinx directives duplicating type annotations
jcfr Mar 25, 2024
1c78838
ENH: Address review
NicerNewerCar Mar 25, 2024
33df368
ENH: Update calibration writer to include comment on clipping-range
NicerNewerCar Apr 3, 2024
d494a89
BUG: Fix generation of camera calibration file
jcfr Apr 18, 2024
80187b0
ENH: Update Autoscoper with vtkCamera schema describing clipping-range
jcfr Apr 18, 2024
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304 changes: 231 additions & 73 deletions AutoscoperM/AutoscoperM.py
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3 changes: 3 additions & 0 deletions AutoscoperM/AutoscoperMLib/IO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,9 @@ def generateCameraCalibrationFile(camera: Camera, filename: str):
contents["view-angle"] = camera.vtkCamera.GetViewAngle()
contents["image-width"] = camera.imageSize[0]
contents["image-height"] = camera.imageSize[1]
# The clipping-range field is not used by Autoscoper, it is used to communicate
# information between AutoscoperM and VirtualRadiographGeneration modules within Slicer.
contents["clipping-range"] = camera.vtkCamera.GetClippingRange()

contents_json = json.dumps(contents, indent=4)

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7 changes: 3 additions & 4 deletions AutoscoperM/AutoscoperMLib/RadiographGeneration.py
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Expand Up @@ -200,7 +200,6 @@ def optimizeCameras(

:return: Optimized cameras
"""
import glob
import os

if not progressCallback:
Expand All @@ -213,11 +212,11 @@ def progressCallback(_x):
cliNodes = []
for i in range(len(cameras)):
camera = cameras[i]
vrgFName = glob.glob(os.path.join(cameraDir, f"cam{camera.id}", "*.tif"))[0]
vrgDirName = os.path.join(cameraDir, f"cam{camera.id}")
cliNode = slicer.cli.run(
cliModule,
None,
{"whiteRadiographFileName": vrgFName},
{"whiteRadiographDirName": vrgDirName},
wait_for_completion=False,
)
cliNodes.append(cliNode)
Expand All @@ -231,7 +230,7 @@ def progressCallback(_x):
slicer.mrmlScene.RemoveNode(cliNode)
raise ValueError("CLI execution failed: " + errorText)
cameras[i].DID = float(cliNodes[i].GetOutputText()) # cliNodes[i].GetParameterAsString("dataIntensityDensity")
progress = ((i + 1) / len(cameras)) * 50 + 40
progress = ((i + 1) / len(cameras)) * 40 + 50
progressCallback(progress)
slicer.mrmlScene.RemoveNode(cliNodes[i])

Expand Down
5 changes: 2 additions & 3 deletions AutoscoperM/AutoscoperMLib/SubVolumeExtraction.py
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Expand Up @@ -246,9 +246,8 @@ def _getItemFromFolder(folderName: str) -> slicer.vtkMRMLNode:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
folderId = shNode.GetItemByName(folderName)
nodeId = shNode.GetItemByPositionUnderParent(folderId, 0)
nodeName = shNode.GetItemName(nodeId)

folderPlugin.setDisplayVisibility(folderId, 1)
slicer.mrmlScene.RemoveNode(slicer.util.getNode(folderName)) # remove the folder
slicer.mrmlScene.RemoveNode(shNode.GetDisplayNodeForItem(folderId)) # remove the folder

return slicer.util.getNode(nodeName) # return the node in the folder
return shNode.GetItemDataNode(nodeId) # return the node in the folder
105 changes: 61 additions & 44 deletions AutoscoperM/Resources/UI/AutoscoperM.ui
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Expand Up @@ -151,6 +151,7 @@
<property name="nodeTypes">
<stringlist notr="true">
<string>vtkMRMLScalarVolumeNode</string>
<string>vtkMRMLSequenceNode</string>
</stringlist>
</property>
<property name="hideChildNodeTypes">
Expand Down Expand Up @@ -210,41 +211,24 @@
<bool>true</bool>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<item row="5" column="2">
<widget class="QSpinBox" name="vrgRes_width">
<property name="maximum">
<number>999999999</number>
</property>
<property name="value">
<number>1760</number>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_13">
<property name="text">
<string>Virtual Radiograph Subdirectory:</string>
</property>
</widget>
</item>
<item row="6" column="2" colspan="2">
<widget class="QLineEdit" name="vrgTempDir">
<item row="3" column="0">
<widget class="QLabel" name="label_14">
<property name="text">
<string>VRG-Temp</string>
<string>Camera Subdirectory:</string>
</property>
</widget>
</item>
<item row="1" column="2" colspan="2">
<widget class="QLineEdit" name="tfmSubDir">
<item row="1" column="0">
<widget class="QLabel" name="label_20">
<property name="text">
<string>Transforms</string>
<string>Partial Volume Transforms Subdirectory:</string>
</property>
</widget>
</item>
<item row="3" column="2" colspan="2">
<widget class="QLineEdit" name="cameraSubDir">
<item row="2" column="0">
<widget class="QLabel" name="label_13">
<property name="text">
<string>Calibration</string>
<string>Virtual Radiograph Subdirectory:</string>
</property>
</widget>
</item>
Expand All @@ -255,24 +239,24 @@
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QLabel" name="label_16">
<item row="5" column="0">
<widget class="QLabel" name="label_15">
<property name="text">
<string>VRG Temp Subdirectory:</string>
<string>VRG Resolution: (width,height)</string>
</property>
</widget>
</item>
<item row="2" column="2" colspan="2">
<widget class="QLineEdit" name="vrgSubDir">
<item row="6" column="2" colspan="2">
<widget class="QLineEdit" name="vrgTempDir">
<property name="text">
<string>RadiographImages</string>
<string>VRG-Temp</string>
</property>
</widget>
</item>
<item row="5" column="0">
<widget class="QLabel" name="label_15">
<item row="2" column="2" colspan="2">
<widget class="QLineEdit" name="vrgSubDir">
<property name="text">
<string>VRG Resolution: (width,height)</string>
<string>RadiographImages</string>
</property>
</widget>
</item>
Expand All @@ -292,17 +276,20 @@
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="label_12">
<item row="6" column="0">
<widget class="QLabel" name="label_16">
<property name="text">
<string>Partial Volume Subdirectory:</string>
<string>VRG Temp Subdirectory:</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_20">
<item row="3" column="2" colspan="2">
<widget class="QLineEdit" name="cameraSubDir">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Partial Volume Transforms Subdirectory:</string>
<string>Calibration</string>
</property>
</widget>
</item>
Expand All @@ -316,10 +303,27 @@
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_14">
<item row="0" column="0">
<widget class="QLabel" name="label_12">
<property name="text">
<string>Camera Subdirectory:</string>
<string>Partial Volume Subdirectory:</string>
</property>
</widget>
</item>
<item row="5" column="2">
<widget class="QSpinBox" name="vrgRes_width">
<property name="maximum">
<number>999999999</number>
</property>
<property name="value">
<number>1760</number>
</property>
</widget>
</item>
<item row="1" column="2" colspan="2">
<widget class="QLineEdit" name="tfmSubDir">
<property name="text">
<string>Transforms</string>
</property>
</widget>
</item>
Expand All @@ -333,6 +337,13 @@
</property>
</widget>
</item>
<item row="9" column="0">
<widget class="QCheckBox" name="idxOnly">
<property name="text">
<string>Only use indices for radiograph filename</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
Expand Down Expand Up @@ -715,6 +726,9 @@
<property name="text">
<string>Flip Y</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="3">
Expand Down Expand Up @@ -749,6 +763,9 @@
<property name="text">
<string>Flip X</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="2">
Expand Down
52 changes: 33 additions & 19 deletions CalculateDataIntensityDensity/CalculateDataIntensityDensity.py
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Original file line number Diff line number Diff line change
@@ -1,34 +1,22 @@
#!/usr/bin/env python-real

import concurrent.futures as cf
import glob
import os
import sys

import numpy as np
import SimpleITK as sitk

def main(whiteRadiographFName: str) -> float:
"""
Calculates the data intensity density of the given camera on its corresponding white radiograph.
Internal function used by :func:`optimizeCameras`.

:param whiteRadiographFName: White radiograph file name

return Data intensity density
"""

import numpy as np
import SimpleITK as sitk

MEAN_COMPARISON = 170 # 255 / 3 * 2

def calcDID(whiteRadiographFName):
MEAN_COMPARISON = 185
# Read in the white radiograph
if not isinstance(whiteRadiographFName, str):
raise TypeError(f"whiteRadiographFName must be a string, not {type(whiteRadiographFName)}")
if not os.path.isfile(whiteRadiographFName):
raise FileNotFoundError(f"File {whiteRadiographFName} not found.")
whiteRadiograph = sitk.ReadImage(whiteRadiographFName)

# Superpixel Segmentation
slicImageFilter = sitk.SLICImageFilter()
slicImageFilter.SetSuperGridSize([15, 15, 15]) # smaller grid size = finer grid overall default is [50,50,50]
slicImageFilter.SetSuperGridSize([85, 85, 85])
labelImage = slicImageFilter.Execute(whiteRadiograph)

# Get the mean pixel value for each label
Expand Down Expand Up @@ -66,6 +54,32 @@ def main(whiteRadiographFName: str) -> float:
return np.sum(sitk.GetArrayFromImage(largest))


def main(whiteRadiographDirName: str) -> float:
"""
Calculates the data intensity density of the given camera on its corresponding white radiograph.
Internal function used by :func:`optimizeCameras`.

:param whiteRadiographFName: White radiograph file name

return Data intensity density
"""
whiteRadiographFiles = glob.glob(os.path.join(whiteRadiographDirName, "*.tif"))

if not isinstance(whiteRadiographDirName, str):
raise TypeError(f"whiteRadiographDirName must be a string, not {type(whiteRadiographDirName)}")
if not os.path.isdir(whiteRadiographDirName):
raise FileNotFoundError(f"Directory {whiteRadiographDirName} not found.")
if len(whiteRadiographFiles) == 0:
raise FileNotFoundError(f"No white radiographs found in {whiteRadiographDirName}")

dids = []
with cf.ThreadPoolExecutor() as executor:
futures = [executor.submit(calcDID, wrFName) for wrFName in whiteRadiographFiles]
for future in cf.as_completed(futures):
dids.append(future.result())
return np.mean(dids)


if __name__ == "__main__":
expected_args = [
"whiteRadiographFileName",
Expand Down
13 changes: 10 additions & 3 deletions CalculateDataIntensityDensity/CalculateDataIntensityDensity.xml
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Expand Up @@ -15,10 +15,10 @@
<acknowledgements><![CDATA[The SlicerAutoscoperM developers gratefully acknowledge funding for this project provided by NIH NIAMS R01AR078924 (Multi-modal Tracking of In Vivo Skeletal Structures and Implants).]]></acknowledgements>
<parameters>
<string>
<name>whiteRadiographFileName</name>
<label>White Radiograph File Name</label>
<name>whiteRadiographDirName</name>
<label>White Radiograph Directory Name</label>
<index>1</index>
<description><![CDATA[Path to the white radiograph used to calculate data intensity density]]></description>
<description><![CDATA[Path to the directory that stores the white radiographs for the current camera, used to calculate data intensity density]]></description>
<channel>input</channel>
</string>
<float>
Expand All @@ -28,6 +28,13 @@
<description><![CDATA[Calculated data intensity density]]></description>
<channel>output</channel>
</float>
<float>
<name>outliers</name>
<label>DID Outliers</label>
<index>3</index>
<description><![CDATA[List of indices that fall outside of the interquartile range]]></description>
<channel>output</channel>
</float>
<label>IO</label>
<description><![CDATA[Input/output parameters]]></description>
</parameters>
Expand Down
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