konfai 1.1.7__py3-none-any.whl → 1.1.9__py3-none-any.whl

{konfai-1.1.7.dist-info → konfai-1.1.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: konfai
-Version: 1.1.7
+Version: 1.1.9
 Summary: Modular and configurable Deep Learning framework with YAML and PyTorch
 Author-email: Valentin Boussot <boussot.v@gmail.com>
 License-Expression: Apache-2.0
@@ -27,8 +27,6 @@ Provides-Extra: lpips
 Requires-Dist: lpips; extra == "lpips"
 Provides-Extra: cluster
 Requires-Dist: submitit; extra == "cluster"
-Provides-Extra: plot
-Requires-Dist: matplotlib; extra == "plot"
 Dynamic: license-file
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/vboussot/KonfAI/blob/main/LICENSE)

konfai-1.1.9.dist-info/RECORD

@@ -0,0 +1,38 @@
+konfai/__init__.py,sha256=qjE9Rqxo1sMrkqGS8I5xlGQMZnjIfU-CGgSI5Wmbmbs,1231
+konfai/evaluator.py,sha256=jsRzVSFjK-V1rZVK9kmN0Gh5-F2JhJrJv291UGNm8CM,16736
+konfai/main.py,sha256=Fc4HcJEhPmgunj_f-QYyvQNvjHrKHSUv27Okgu6V5_A,3842
+konfai/predictor.py,sha256=k9S-AH-wGvmr4YQF2IczJ2Nb9_aTZwNd9f6iu4s9v78,34591
+konfai/trainer.py,sha256=wNHgDh0LtxTi0-aWCkT90hjjpJFaX_zRWyA5esVrsLY,28072
+konfai/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+konfai/data/augmentation.py,sha256=vcJE7mosvUkwbpbTN_lGP0S1uJrJYGjlLrt9VnDdJYY,27792
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+konfai/data/transform.py,sha256=MmA1vgXAj1V-e-8RNa1XAaHbWI5i85NoVyCp7yZ2-kg,26816
+konfai/metric/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+konfai/metric/schedulers.py,sha256=TpYMA24FMpxRnqfhMGb0i_Mm-bzT9kySbBgvkYk-6wM,1327
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+konfai-1.1.9.dist-info/RECORD,,

konfai/utils/registration.py

@@ -1,199 +0,0 @@
-import SimpleITK as sitk
-from typing import Union
-import numpy as np
-import sys
-import scipy
-
-def parameterMap_to_transform(path_src: str) -> Union[sitk.Transform, list[sitk.Transform]]:
-    transform = sitk.ReadParameterFile(path_src)
-    format = lambda x: [float(i) for i in x]
-    dimension = int(transform["FixedImageDimension"][0])
-
-    if transform["Transform"][0] == "EulerTransform":
-        if dimension == 2:
-            result = sitk.Euler2DTransform()
-        else:
-            result = sitk.Euler3DTransform()
-        parameters = format(transform["TransformParameters"])
-        fixedParameters = format(transform["CenterOfRotationPoint"])+[0]
-    elif transform["Transform"][0] == "TranslationTransform":
-        result = sitk.TranslationTransform(dimension)
-        parameters = format(transform["TransformParameters"])
-        fixedParameters = []
-    elif transform["Transform"][0] == "AffineTransform":
-        result = sitk.AffineTransform(dimension)
-        parameters = format(transform["TransformParameters"])
-        fixedParameters = format(transform["CenterOfRotationPoint"])+[0]
-    elif transform["Transform"][0] == "BSplineStackTransform":
-        parameters = format(transform["TransformParameters"])
-        GridSize = format(transform["GridSize"])
-        GridOrigin = format(transform["GridOrigin"])
-        GridSpacing = format(transform["GridSpacing"])
-        GridDirection =  np.asarray(format(transform["GridDirection"])).reshape((dimension, dimension)).T.flatten() 
-        fixedParameters = np.concatenate([GridSize, GridOrigin, GridSpacing, GridDirection])
-
-        nb = int(format(transform["Size"])[-1])
-        sub = int(np.prod(GridSize))*dimension
-        results = []
-        for i in range(nb):
-            result = sitk.BSplineTransform(dimension)
-            sub_parameters = np.asarray(parameters[i*sub:(i+1)*sub])
-            result.SetFixedParameters(fixedParameters)
-            result.SetParameters(sub_parameters)
-            results.append(result)
-        return results
-    elif transform["Transform"][0] == "AffineLogStackTransform":
-        parameters = format(transform["TransformParameters"])
-        fixedParameters = format(transform["CenterOfRotationPoint"])+[0]
-
-        nb = int(transform["NumberOfSubTransforms"][0])
-        sub = dimension*4
-        results = []
-        for i in range(nb):
-            result = sitk.AffineTransform(dimension)
-            sub_parameters = np.asarray(parameters[i*sub:(i+1)*sub])
-
-            result.SetFixedParameters(fixedParameters)
-            result.SetParameters(np.concatenate([scipy.linalg.expm(sub_parameters[:dimension*dimension].reshape((dimension,dimension))).flatten(), sub_parameters[-dimension:]]))
-            results.append(result)
-        return results
-    else:
-        result = sitk.BSplineTransform(dimension)
-        
-        parameters = format(transform["TransformParameters"])
-        GridSize = format(transform["GridSize"])
-        GridOrigin = format(transform["GridOrigin"])
-        GridSpacing = format(transform["GridSpacing"])
-        GridDirection = np.array(format(transform["GridDirection"])).reshape((dimension,dimension)).T.flatten() 
-        fixedParameters = np.concatenate([GridSize, GridOrigin, GridSpacing, GridDirection])
-
-    result.SetFixedParameters(fixedParameters)
-    result.SetParameters(parameters)
-    return result
-
-if __name__ == "__main__":
-    out_path = sys.argv[1]
-    finename = sys.argv[2]
-    finename_dest = sys.argv[3]
-    transform = parameterMap_to_transform("{}/{}".format(out_path, finename))
-    sitk.WriteTransform(transform, "{}/{}".format(out_path, finename_dest))
-
-def getFlatLabel(mask: sitk.Image, labels: list[int]) -> sitk.Image:
-    data = sitk.GetArrayFromImage(mask)
-    result_data = np.zeros_like(data, np.uint8)
-
-    for label in labels:
-        result_data[data == label] = 1
-
-    result = sitk.GetImageFromArray(result_data)
-    result.CopyInformation(mask)        
-    return result
-
-def rampFilterHistogram(image: sitk.Image, rampStart: float, rampEnd: float) -> sitk.Image:
-    imageData = sitk.GetArrayFromImage(image)
-    filter = np.logical_and(imageData > rampStart, imageData < rampEnd)
-    rampWidth = rampEnd - rampStart
-    imageData[filter] = (1/rampWidth) * (imageData[filter] - rampStart) * imageData[filter]
-    filteredImage = sitk.GetImageFromArray(imageData)
-    filteredImage.CopyInformation(image)
-    return filteredImage
-
-def elastic_registration(   fixed_image : sitk.Image,
-                            moving_image : sitk.Image,
-                            fixed_mask : Union[sitk.Image, None],
-                            moving_mask : Union[sitk.Image, None],
-                            name_parameterMap : str,
-                            outputDir: str) -> sitk.Transform:
-        labels = np.unique(sitk.GetArrayFromImage(fixed_mask))
-        fixed_mask = getFlatLabel(fixed_mask, labels[1:])
-        moving_mask = getFlatLabel(moving_mask, labels[1:])
-
-        fixed_mask.CopyInformation(fixed_image)
-        moving_mask.CopyInformation(moving_image)
-
-        fixed_mask_dillated = sitk.BinaryDilate(fixed_mask, [5,5,5])
-        moving_mask_dillated = sitk.BinaryDilate(moving_mask, [5,5,5])
-        
-        fixed_image = sitk.Mask(fixed_image, fixed_mask)
-        moving_image = sitk.Mask(moving_image, moving_mask)
-
-
-        minGradientMagnitude = 50
-        fixed_image_gradient = rampFilterHistogram(sitk.VectorMagnitude(sitk.Gradient(fixed_image)), 0, minGradientMagnitude)
-        moving_image_gradient = rampFilterHistogram(sitk.VectorMagnitude(sitk.Gradient(moving_image)), 0, minGradientMagnitude)
-
-        elastixImageFilter = sitk.ElastixImageFilter()
-        elastixImageFilter.SetFixedImage(fixed_image_gradient)
-        elastixImageFilter.AddFixedImage(fixed_image)
-        elastixImageFilter.AddFixedImage(fixed_image)
-
-        if fixed_mask is not None:
-            elastixImageFilter.SetFixedMask(fixed_mask)
-            elastixImageFilter.AddFixedMask(fixed_mask_dillated)
-            elastixImageFilter.AddFixedMask(fixed_mask_dillated)
-
-
-        elastixImageFilter.SetMovingImage(moving_image_gradient)
-        elastixImageFilter.AddMovingImage(moving_image)
-        elastixImageFilter.AddMovingImage(moving_image)
-        
-        if moving_mask is not None:
-            elastixImageFilter.SetMovingMask(moving_mask)
-            elastixImageFilter.AddMovingMask(moving_mask_dillated)
-            elastixImageFilter.AddMovingMask(moving_mask_dillated)
-
-        elastixImageFilter.SetParameterMap(sitk.ReadParameterFile("{}.txt".format(name_parameterMap)))
-        elastixImageFilter.LogToConsoleOn()
-        elastixImageFilter.SetOutputDirectory(outputDir)
-        
-        elastixImageFilter.Execute()
-        
-        transform = parameterMap_to_transform("{}TransformParameters".format(outputDir))
-        
-        return transform
-
-def registration(   fixed_image : sitk.Image,
-                    moving_image : sitk.Image,
-                    fixed_mask : Union[sitk.Image, None],
-                    moving_mask : Union[sitk.Image, None],
-                    name_parameterMap : str,
-                    outputDir: str) -> sitk.Transform:
-        elastixImageFilter = sitk.ElastixImageFilter()
-        elastixImageFilter.SetFixedImage(fixed_image)
-        if fixed_mask is not None:
-            elastixImageFilter.SetFixedMask(fixed_mask)
-
-        elastixImageFilter.SetMovingImage(moving_image)
-        if moving_mask is not None:
-            elastixImageFilter.SetMovingMask(moving_mask)
-
-        elastixImageFilter.SetParameterMap(sitk.ReadParameterFile("{}.txt".format(name_parameterMap)))
-        elastixImageFilter.LogToConsoleOn()
-        elastixImageFilter.SetOutputDirectory(outputDir)
-        elastixImageFilter.Execute()
-        
-        transform = parameterMap_to_transform("{}TransformParameters".format(outputDir))
-        
-        return transform
-
-def registration_groupewise(images_1: sitk.Image, masks: sitk.Image, images_2: sitk.Image, name_parameterMap : str, output_dir: str):
-    elastixImageFilter = sitk.ElastixImageFilter()
-    elastixImageFilter.SetFixedImage(images_1)
-    elastixImageFilter.SetMovingImage(images_1)
-    elastixImageFilter.SetFixedMask(masks)
-    elastixImageFilter.SetMovingMask(masks)
-    
-    if images_2 is not None:
-        elastixImageFilter.AddFixedImage(images_2)
-        elastixImageFilter.AddMovingImage(images_2)
-        #elastixImageFilter.AddFixedImage(images_2)
-        #elastixImageFilter.AddMovingImage(images_2)
-    
-    elastixImageFilter.SetParameterMap(sitk.ReadParameterFile("{}.txt".format(name_parameterMap)))
-    elastixImageFilter.LogToConsoleOn()
-    elastixImageFilter.SetOutputDirectory(output_dir)
-    elastixImageFilter.LogToFileOn()
-    elastixImageFilter.Execute()
-
-    transforms = parameterMap_to_transform("{}TransformParameters".format(output_dir))
-    return transforms

konfai-1.1.7.dist-info/RECORD

@@ -1,39 +0,0 @@
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