biomedisa 2024.5.18__py3-none-any.whl → 2024.5.20__py3-none-any.whl

biomedisa-2024.5.20.dist-info/RECORD

@@ -0,0 +1,44 @@
+biomedisa/__init__.py,sha256=RxXuOh-e-W9k7pvmKDyYZz3bbze7AkB7RgRpUCzLbcE,1538
+biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
+biomedisa/deeplearning.py,sha256=dVwLkijm0ibtn6zUUV3t2WK6Fzvks4VlgzKNLqzDpAQ,27064
+biomedisa/interpolation.py,sha256=R8UbBWt7vOuiQCPSeNIpEY0_yfQUg1oBfhAjXi91Hl4,17253
+biomedisa/mesh.py,sha256=glvpTN0PPByb5j2IbLCdWQtc5O4VT-Pwu3en8EaYyTo,15819
+biomedisa/features/DataGenerator.py,sha256=bGys6UZ0bnKb_k1Y3Spo6MNPk_goSAmptdZnI39smaw,12770
+biomedisa/features/DataGeneratorCrop.py,sha256=23R4Z-8tB1CsjYTYfhHGovlJpAny_q9OV9hq8kc2GJg,5454
+biomedisa/features/PredictDataGenerator.py,sha256=JH8SPGQm-Y7_Drec2fw3jBUupvpIkQ1FvkDXP7mUjDY,4074
+biomedisa/features/PredictDataGeneratorCrop.py,sha256=HF5tJbGtlJMHr7lMT9IiIdLG2CTjXstbKoOjlZJ93Is,3431
+biomedisa/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biomedisa/features/active_contour.py,sha256=n5_vAD8jvQjU6fQ6A9hxjSmtkLLo_1fl0S5q1H2pmVg,18096
+biomedisa/features/assd.py,sha256=q9NUQXEoA4Pi3d8b5fmys615CWu06Sm0N9-OGwJOFnw,6537
+biomedisa/features/biomedisa_helper.py,sha256=iLbt4RpCU3EK51uiMefkM0321AgBdeLgrT-X4d--YJY,32250
+biomedisa/features/create_slices.py,sha256=tLDJmuJFN8teTiCYvMauExfVzT2ZUF28VcPXpo4sOsE,13001
+biomedisa/features/crop_helper.py,sha256=si72n9Q-C7U0cXYOD9Ux2UqIbZdXbZSOARBYDeqRggI,24533
+biomedisa/features/curvop_numba.py,sha256=AjKQJcUBoURTB8pq1HmugQYpBwBELthhcEu51_r_xPI,7049
+biomedisa/features/django_env.py,sha256=pdiPcBpqu1BWuyvh-palIGVwHFaY-leQ4Gatlbm8hIg,8942
+biomedisa/features/keras_helper.py,sha256=1rM5-fMj71oW99VxEt2U3SZey1EbO9q5CNVJlmN6YxA,50250
+biomedisa/features/nc_reader.py,sha256=RoRMwu3ELSNfoV3qZtaT2OWACnXb2EhNFu_DAF1T93o,7406
+biomedisa/features/pid.py,sha256=Jmn1VIp0fBlgBrqZ-yUIQVVb5-NAxNBdibXALVr2PPI,2545
+biomedisa/features/process_image.py,sha256=VtS3fGDvglqJiiJLPK1toe76J58j914NJ8XQKg3CRwo,11091
+biomedisa/features/pycuda_test.py,sha256=UGAGIz_dgcCJkzjyCqnMlflp-WJPzpCtFQmE9C5DwIo,3275
+biomedisa/features/remove_outlier.py,sha256=XhbFPkazMmEUZiP0FERdCkrXaLhwO095x4wcn-B3SdU,16756
+biomedisa/features/split_volume.py,sha256=l106WXlDSDut-PlP9_O7WmJCp6euoViPjYG7awoA9Y8,8926
+biomedisa/features/amira_to_np/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biomedisa/features/amira_to_np/amira_data_stream.py,sha256=JrZTyKP01CKDFB5d9BlGtSFwBgoAo0AJeAmn3pADH88,32618
+biomedisa/features/amira_to_np/amira_grammar.py,sha256=z1yajLHmn-GDb-rzZ5iHlKmPZDDbO9fNqP2jXf8z3KE,14324
+biomedisa/features/amira_to_np/amira_header.py,sha256=eWHECsTx3ls8c0RHjy5xO4s-BehRC-96wONj7n9IzrY,11553
+biomedisa/features/amira_to_np/amira_helper.py,sha256=giuZKkX8eI_2MVAy3wwBvcmmmDxSOo8k9eAzu2QA6uo,2218
+biomedisa/features/random_walk/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biomedisa/features/random_walk/gpu_kernels.py,sha256=IQDjq1H6iJCwdS-LCWx2S6F1TMEXjrN2veLcTLCeCoI,7191
+biomedisa/features/random_walk/pycuda_large.py,sha256=Vfvd0uFRB-qLReDFKIyAAhdWDLflKMUEUAm_ZXSkPZs,32917
+biomedisa/features/random_walk/pycuda_large_allx.py,sha256=zjy1Ai8D-foXjaT-6G33vGMANS1i00BBbLCTAMUfP5c,30677
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+biomedisa/features/random_walk/pyopencl_large.py,sha256=q79AxG3p3qFjxfiAZfUK9I5BAYT2prq48yEEmpP1Yjk,31015
+biomedisa/features/random_walk/pyopencl_small.py,sha256=opNlS-qzOa9qWafBNJdvf6r1aRAFf7_JXf6ISDnkdXE,17068
+biomedisa/features/random_walk/rw_large.py,sha256=ZnITvk00Y11ZZlGuBRaJO1EwU0wYBdEwdpj9vvXCqF4,19805
+biomedisa/features/random_walk/rw_small.py,sha256=RPzZe24YrEwYelJukDjvqaoD_SyhgdriEi7uV3kZGXI,14881
+biomedisa-2024.5.20.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-2024.5.20.dist-info/METADATA,sha256=uM3KiOS5fzl6WFv8cNRgsCT-l4DnGzgZoBiDqPg_qXM,10677
+biomedisa-2024.5.20.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+biomedisa-2024.5.20.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-2024.5.20.dist-info/RECORD,,

biomedisa/biomedisa_features/split_volume.py

@@ -1,274 +0,0 @@
-##########################################################################
-##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
-##                                                                      ##
-##  This file is part of the open source project biomedisa.             ##
-##                                                                      ##
-##  Licensed under the European Union Public Licence (EUPL)             ##
-##  v1.2, or - as soon as they will be approved by the                  ##
-##  European Commission - subsequent versions of the EUPL;              ##
-##                                                                      ##
-##  You may redistribute it and/or modify it under the terms            ##
-##  of the EUPL v1.2. You may not use this work except in               ##
-##  compliance with this Licence.                                       ##
-##                                                                      ##
-##  You can obtain a copy of the Licence at:                            ##
-##                                                                      ##
-##  https://joinup.ec.europa.eu/page/eupl-text-11-12                    ##
-##                                                                      ##
-##  Unless required by applicable law or agreed to in                   ##
-##  writing, software distributed under the Licence is                  ##
-##  distributed on an "AS IS" basis, WITHOUT WARRANTIES                 ##
-##  OR CONDITIONS OF ANY KIND, either express or implied.               ##
-##                                                                      ##
-##  See the Licence for the specific language governing                 ##
-##  permissions and limitations under the Licence.                      ##
-##                                                                      ##
-##########################################################################
-
-import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-sys.path.append(BASE_DIR)
-from biomedisa_features.biomedisa_helper import load_data, save_data
-import numpy as np
-import subprocess
-import platform
-import glob
-
-if __name__ == '__main__':
-
-    # path to data
-    path_to_data = sys.argv[1]
-    path_to_labels = sys.argv[2]
-
-    # get arguments
-    nump = 1
-    smooth = 0
-    overlap = 100
-    sub_z, sub_y, sub_x = 1, 1, 1
-    for i, val in enumerate(sys.argv):
-        if val in ['--split_z','-sz']:
-            sub_z = max(int(sys.argv[i+1]), 1)
-        if val in ['--split_y','-sy']:
-            sub_y = max(int(sys.argv[i+1]), 1)
-        if val in ['--split_x','-sx']:
-            sub_x = max(int(sys.argv[i+1]), 1)
-        if val in ['--overlap','-ol']:
-            overlap = max(int(sys.argv[i+1]), 0)
-        if val in ['-n','-np']:
-            nump = max(int(sys.argv[i+1]), 1)
-        if val in ['--smooth','-s']:
-            smooth = int(sys.argv[i+1])
-    uq = True if any(x in sys.argv for x in ['--uncertainty','-uq']) else False
-    allx = 1 if '-allx' in sys.argv else 0
-
-    # base directory
-    BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-
-    # clean tmp folder
-    filelist = glob.glob(BASE_DIR+'/tmp/*.tif')
-    for f in filelist:
-        os.remove(f)
-
-    # data shape
-    data, _ = load_data(path_to_data, 'split_volume')
-    shape = np.copy(np.array(data.shape), order='C')
-    zsh, ysh, xsh = shape
-    del data
-
-    # split volume
-    sub_size_z = np.ceil(zsh / sub_z)
-    sub_size_y = np.ceil(ysh / sub_y)
-    sub_size_x = np.ceil(xsh / sub_x)
-
-    # iterate over subvolumes
-    for sub_z_i in range(sub_z):
-        for sub_y_i in range(sub_y):
-            for sub_x_i in range(sub_x):
-                subvolume = sub_z_i*sub_y*sub_x + sub_y_i*sub_x + sub_x_i + 1
-                print('Subvolume:', subvolume, '/', sub_z*sub_y*sub_x)
-
-                # determine z subvolume
-                blockmin_z = int(sub_z_i * sub_size_z)
-                blockmax_z = int((sub_z_i+1) * sub_size_z)
-                datamin_z = max(blockmin_z - overlap, 0)
-                datamax_z = min(blockmax_z + overlap, zsh)
-
-                # determine y subvolume
-                blockmin_y = int(sub_y_i * sub_size_y)
-                blockmax_y = int((sub_y_i+1) * sub_size_y)
-                datamin_y = max(blockmin_y - overlap, 0)
-                datamax_y = min(blockmax_y + overlap, ysh)
-
-                # determine x subvolume
-                blockmin_x = int(sub_x_i * sub_size_x)
-                blockmax_x = int((sub_x_i+1) * sub_size_x)
-                datamin_x = max(blockmin_x - overlap, 0)
-                datamax_x = min(blockmax_x + overlap, xsh)
-
-                # extract image subvolume
-                data, _ = load_data(path_to_data, 'split_volume')
-                save_data(BASE_DIR+f'/tmp/sub_volume_{subvolume}.tif', data[datamin_z:datamax_z,datamin_y:datamax_y,datamin_x:datamax_x], False)
-                del data
-
-                # extract label subvolume
-                labelData, header, final_image_type = load_data(path_to_labels, 'split_volume', True)
-                save_data(BASE_DIR+'/tmp/labels.sub_volume.tif', labelData[datamin_z:datamax_z,datamin_y:datamax_y,datamin_x:datamax_x])
-                del labelData
-
-                # configure command
-                cmd = ['mpiexec', '-np', f'{nump}', 'python3', 'biomedisa_interpolation.py', BASE_DIR+f'/tmp/sub_volume_{subvolume}.tif', BASE_DIR+'/tmp/labels.sub_volume.tif', '-s', f'{smooth}']
-                if uq:
-                    cmd.append('-uq')
-                if allx:
-                    cmd.append('-allx')
-                cwd = BASE_DIR + '/demo/'
-
-                # run segmentation
-                if platform.system() == 'Windows':
-                    cmd[3] = 'python'
-                    cmd.insert(4, '-u')
-                    p = subprocess.Popen(cmd, cwd=cwd, stdout=subprocess.PIPE)
-                    for line in iter(p.stdout.readline, b''):
-                        line = str(line,'utf-8')
-                        print(line.rstrip())
-                    p.stdout.close()
-                else:
-                    p = subprocess.Popen(cmd, cwd=cwd)
-                p.wait()
-
-                # remove tmp files
-                os.remove(BASE_DIR+f'/tmp/sub_volume_{subvolume}.tif')
-                os.remove(BASE_DIR+'/tmp/labels.sub_volume.tif')
-
-    # create path_to_final
-    filename, extension = os.path.splitext(os.path.basename(path_to_data))
-    if extension == '.gz':
-        filename = filename[:-4]
-    filename = 'final.' + filename
-    path_to_final = path_to_data.replace(os.path.basename(path_to_data), filename + final_image_type)
-
-    # path_to_uq and path_to_smooth
-    filename, extension = os.path.splitext(path_to_final)
-    if extension == '.gz':
-        filename = filename[:-4]
-    path_to_smooth = filename + '.smooth' + final_image_type
-    path_to_uq = filename + '.uncertainty.tif'
-
-    # iterate over subvolumes
-    final = np.zeros((zsh, ysh, xsh), dtype=np.uint8)
-    for sub_z_i in range(sub_z):
-        for sub_y_i in range(sub_y):
-            for sub_x_i in range(sub_x):
-                subvolume = sub_z_i*sub_y*sub_x + sub_y_i*sub_x + sub_x_i + 1
-                print('Subvolume:', subvolume, '/', sub_z*sub_y*sub_x)
-
-                # determine z subvolume
-                blockmin_z = int(sub_z_i * sub_size_z)
-                blockmax_z = int((sub_z_i+1) * sub_size_z)
-                datamin_z = max(blockmin_z - overlap, 0)
-                datamax_z = min(blockmax_z + overlap, zsh)
-
-                # determine y subvolume
-                blockmin_y = int(sub_y_i * sub_size_y)
-                blockmax_y = int((sub_y_i+1) * sub_size_y)
-                datamin_y = max(blockmin_y - overlap, 0)
-                datamax_y = min(blockmax_y + overlap, ysh)
-
-                # determine x subvolume
-                blockmin_x = int(sub_x_i * sub_size_x)
-                blockmax_x = int((sub_x_i+1) * sub_size_x)
-                datamin_x = max(blockmin_x - overlap, 0)
-                datamax_x = min(blockmax_x + overlap, xsh)
-
-                # load subvolume
-                path_to_subvolume = BASE_DIR+f'/tmp/final.sub_volume_{subvolume}.tif'
-                if os.path.isfile(path_to_subvolume):
-                    tmp, _ = load_data(path_to_subvolume)
-                    final[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
-                    = tmp[blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
-                    os.remove(path_to_subvolume)
-
-    # save result
-    save_data(path_to_final, final, header)
-
-    # iterate over subvolumes (smooth)
-    smooth = 0
-    final.fill(0)
-    for sub_z_i in range(sub_z):
-        for sub_y_i in range(sub_y):
-            for sub_x_i in range(sub_x):
-                subvolume = sub_z_i*sub_y*sub_x + sub_y_i*sub_x + sub_x_i + 1
-                print('Subvolume:', subvolume, '/', sub_z*sub_y*sub_x)
-
-                # determine z subvolume
-                blockmin_z = int(sub_z_i * sub_size_z)
-                blockmax_z = int((sub_z_i+1) * sub_size_z)
-                datamin_z = max(blockmin_z - overlap, 0)
-                datamax_z = min(blockmax_z + overlap, zsh)
-
-                # determine y subvolume
-                blockmin_y = int(sub_y_i * sub_size_y)
-                blockmax_y = int((sub_y_i+1) * sub_size_y)
-                datamin_y = max(blockmin_y - overlap, 0)
-                datamax_y = min(blockmax_y + overlap, ysh)
-
-                # determine x subvolume
-                blockmin_x = int(sub_x_i * sub_size_x)
-                blockmax_x = int((sub_x_i+1) * sub_size_x)
-                datamin_x = max(blockmin_x - overlap, 0)
-                datamax_x = min(blockmax_x + overlap, xsh)
-
-                # load subvolume
-                path_to_subvolume = BASE_DIR+f'/tmp/final.sub_volume_{subvolume}.smooth.tif'
-                if os.path.isfile(path_to_subvolume):
-                    tmp, _ = load_data(path_to_subvolume)
-                    final[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
-                    = tmp[blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
-                    os.remove(path_to_subvolume)
-                    smooth = 1
-
-    # save result
-    if smooth:
-        save_data(path_to_smooth, final, header)
-
-    # iterate over subvolumes (uncertainty)
-    uncertainty = 0
-    final.fill(0)
-    for sub_z_i in range(sub_z):
-        for sub_y_i in range(sub_y):
-            for sub_x_i in range(sub_x):
-                subvolume = sub_z_i*sub_y*sub_x + sub_y_i*sub_x + sub_x_i + 1
-                print('Subvolume:', subvolume, '/', sub_z*sub_y*sub_x)
-
-                # determine z subvolume
-                blockmin_z = int(sub_z_i * sub_size_z)
-                blockmax_z = int((sub_z_i+1) * sub_size_z)
-                datamin_z = max(blockmin_z - overlap, 0)
-                datamax_z = min(blockmax_z + overlap, zsh)
-
-                # determine y subvolume
-                blockmin_y = int(sub_y_i * sub_size_y)
-                blockmax_y = int((sub_y_i+1) * sub_size_y)
-                datamin_y = max(blockmin_y - overlap, 0)
-                datamax_y = min(blockmax_y + overlap, ysh)
-
-                # determine x subvolume
-                blockmin_x = int(sub_x_i * sub_size_x)
-                blockmax_x = int((sub_x_i+1) * sub_size_x)
-                datamin_x = max(blockmin_x - overlap, 0)
-                datamax_x = min(blockmax_x + overlap, xsh)
-
-                # load subvolume
-                path_to_subvolume = BASE_DIR+f'/tmp/final.sub_volume_{subvolume}.uncertainty.tif'
-                if os.path.isfile(path_to_subvolume):
-                    tmp, _ = load_data(path_to_subvolume)
-                    final[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
-                    = tmp[blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
-                    os.remove(path_to_subvolume)
-                    uncertainty = 1
-
-    # save result
-    if uncertainty:
-        save_data(path_to_uq, final, header)
-

biomedisa-2024.5.18.dist-info/RECORD

@@ -1,44 +0,0 @@
-biomedisa/__init__.py,sha256=BLbuGv-c8I8XMzOOnc07qrcWxq8CUA5NM73S3gkixEI,1690
-biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
-biomedisa/deeplearning.py,sha256=eobgRva1ucb1IKpj7SNxmBOsWdZCPAJ-BNbIKnApNeA,27063
-biomedisa/interpolation.py,sha256=mz5Ieiee2RftqisqNzKcCU7IV1n0LGON4zyhvBwE94s,17335
-biomedisa/mesh.py,sha256=6f5klVPoA3zmF3jxLCOUkCXelLtlroS6tJquRHaMwsQ,15920
-biomedisa/biomedisa_features/DataGenerator.py,sha256=FTktX35_FboSzk4UXG_ZN58xXYJqwjX_7ZJ65bzNuFs,12770
-biomedisa/biomedisa_features/DataGeneratorCrop.py,sha256=cL_1rbXSq79vCNAHnIwvow-J1s-4gWStR1pWTbF_VTY,5454
-biomedisa/biomedisa_features/PredictDataGenerator.py,sha256=MISkB2tlxCw6rd8pfwwz1clVnvyPwg5dB-8yxR6WsBw,4074
-biomedisa/biomedisa_features/PredictDataGeneratorCrop.py,sha256=JBwFcOZMakNMlL5UvP5bNg9FlQl5sbrM9UVSCyFhwBQ,3431
-biomedisa/biomedisa_features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biomedisa/biomedisa_features/active_contour.py,sha256=PUAfCzHKU-p7xeQoWxmDh0ZFbnInXEsafgeE1k-96d0,18131
-biomedisa/biomedisa_features/assd.py,sha256=cXHAhwJqhwOvzgTodlQb21NvYafWTjBJ7_H_icuBNMU,6537
-biomedisa/biomedisa_features/biomedisa_helper.py,sha256=fY7kHLg5VBLF4f_W-p9tZaeqZn6wCq9OHPImZC41GRU,32401
-biomedisa/biomedisa_features/create_slices.py,sha256=gQJev1-DXvqDchGbnLC1bsCtb1gAnv4D82IgOnCJVt8,13329
-biomedisa/biomedisa_features/crop_helper.py,sha256=Op8x10IltAR_5YMotuVHzF3hSbxiOkAchhJM5L0qutw,23894
-biomedisa/biomedisa_features/curvop_numba.py,sha256=9jc4OvHQ6JDN-DaFhRQMLpBDU85HhqzX_YUVBf3Q3vA,7049
-biomedisa/biomedisa_features/django_env.py,sha256=S-ajQpw5A2aBlTYgn_FiyIr02QH05rInzhBDulb9lNg,8989
-biomedisa/biomedisa_features/keras_helper.py,sha256=J4VZNPgdoQSH5wnCcdkubRhxquNmPOUzEAlSkTZltuw,50343
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