biomedisa 24.5.23__py3-none-any.whl

biomedisa/interpolation.py

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+#!/usr/bin/python3
+##########################################################################
+##                                                                      ##
+##  Copyright (c) 2019-2024 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 os
+import biomedisa
+from biomedisa.features.biomedisa_helper import (_get_platform, smooth_img_3x3,
+    pre_processing, _error_, read_labeled_slices, read_labeled_slices_allx,
+    read_indices_allx, predict_blocksize)
+from multiprocessing import freeze_support
+import numpy as np
+import argparse
+import time
+
+class Biomedisa(object):
+     pass
+
+def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_alpha=1.0, acwe_smooth=1, acwe_steps=3,
+    path_to_data=None, path_to_labels=None, denoise=False, uncertainty=False, platform=None,
+    allaxis=False, ignore='none', only='all', smooth=0, no_compression=False, return_hits=False,
+    img_id=None, label_id=None, remote=False, queue=0, clean=None, fill=None):
+
+    freeze_support()
+
+    from mpi4py import MPI
+    comm = MPI.COMM_WORLD
+    rank = comm.Get_rank()
+    size = comm.Get_size()
+
+    if rank == 0:
+
+        # create biomedisa
+        bm = Biomedisa()
+        bm.process = 'smart_interpolation'
+        bm.success = True
+
+        # time
+        bm.TIC = time.time()
+
+        # transfer arguments
+        key_copy = tuple(locals().keys())
+        for arg in key_copy:
+            bm.__dict__[arg] = locals()[arg]
+
+        # django environment
+        if bm.img_id is not None:
+            bm.django_env = True
+        else:
+            bm.django_env = False
+
+        # compression
+        if no_compression:
+            bm.compression = False
+        else:
+            bm.compression = True
+
+        # disable file saving when called as a function
+        if bm.data is not None:
+            bm.path_to_data = None
+            bm.path_to_labels = None
+
+        # set pid and write in logfile
+        if bm.django_env:
+            from biomedisa.features.django_env import create_pid_object
+            create_pid_object(os.getpid(), bm.remote, bm.queue, bm.img_id)
+
+            # write in logfile
+            bm.username = os.path.basename(os.path.dirname(bm.path_to_data))
+            bm.shortfilename = os.path.basename(bm.path_to_data)
+            bm.path_to_logfile = biomedisa.BASE_DIR + '/log/logfile.txt'
+            bm.path_to_time = biomedisa.BASE_DIR + '/log/time.txt'
+            with open(bm.path_to_logfile, 'a') as logfile:
+                print('%s %s %s %s' %(time.ctime(), bm.username, bm.shortfilename, 'Process was started.'), file=logfile)
+
+        # pre-processing
+        bm = pre_processing(bm)
+
+        # get platform
+        if bm.success:
+            if bm.platform == 'cuda_force':
+                bm.platform = 'cuda'
+            else:
+                bm = _get_platform(bm)
+                if bm.success == False:
+                    bm = _error_(bm, f'No {bm.platform} device found.')
+
+        # smooth, uncertainty and allx are not supported for opencl
+        if bm.success and bm.platform.split('_')[0] == 'opencl':
+            if bm.smooth:
+                bm.smooth = 0
+                print('Warning: Smoothing is not yet supported for opencl. Process starts without smoothing.')
+            if bm.uncertainty:
+                bm.uncertainty = False
+                print('Warning: Uncertainty is not yet supported for opencl. Process starts without uncertainty.')
+            if bm.allaxis:
+                bm = _error_(bm, 'Allx is not yet supported for opencl.')
+
+        if not bm.success:
+
+            # send not executable
+            for dest in range(1, size):
+                comm.send(bm.success, dest=dest, tag=0)
+
+        else:
+
+            # create path_to_final
+            if bm.path_to_data:
+                filename, extension = os.path.splitext(os.path.basename(bm.path_to_data))
+                if extension == '.gz':
+                    filename = filename[:-4]
+                filename = 'final.' + filename
+                bm.path_to_final = bm.path_to_data.replace(os.path.basename(bm.path_to_data), filename + bm.final_image_type)
+
+                # paths to optional results
+                filename, extension = os.path.splitext(bm.path_to_final)
+                if extension == '.gz':
+                    filename = filename[:-4]
+                bm.path_to_smooth = filename + '.smooth' + bm.final_image_type
+                bm.path_to_smooth_cleaned = filename + '.smooth.cleand' + bm.final_image_type
+                bm.path_to_cleaned = filename + '.cleaned' + bm.final_image_type
+                bm.path_to_filled = filename + '.filled' + bm.final_image_type
+                bm.path_to_cleaned_filled = filename + '.cleaned.filled' + bm.final_image_type
+                bm.path_to_refined = filename + '.refined' + bm.final_image_type
+                bm.path_to_acwe = filename + '.acwe' + bm.final_image_type
+                bm.path_to_uq = filename + '.uncertainty.tif'
+
+            # data type
+            if bm.data.dtype == 'uint8':
+                pass
+            elif bm.data.dtype == 'int8':
+                bm.data = bm.data.astype(np.int16)
+                bm.data += 128
+                bm.data = bm.data.astype(np.uint8)
+            else:
+                bm.data = bm.data.astype(float)
+                bm.data -= np.amin(bm.data)
+                bm.data /= np.amax(bm.data)
+                bm.data *= 255.0
+                bm.data = bm.data.astype(np.float32)
+
+            # denoise image data
+            if bm.denoise:
+                bm.data = smooth_img_3x3(bm.data)
+
+            # image size
+            bm.imageSize = int(bm.data.nbytes * 10e-7)
+
+            # add boundaries
+            zsh, ysh, xsh = bm.data.shape
+            tmp = np.zeros((1+zsh+1, 1+ysh+1, 1+xsh+1), dtype=bm.labelData.dtype)
+            tmp[1:-1, 1:-1, 1:-1] = bm.labelData
+            bm.labelData = tmp.copy(order='C')
+            tmp = np.zeros((1+zsh+1, 1+ysh+1, 1+xsh+1), dtype=bm.data.dtype)
+            tmp[1:-1, 1:-1, 1:-1] = bm.data
+            bm.data = tmp.copy(order='C')
+            bm.zsh, bm.ysh, bm.xsh = bm.data.shape
+
+            # check if labeled slices are adjacent
+            if bm.allaxis:
+                bm.indices = []
+                indices_tmp = read_indices_allx(bm.labelData, 0)
+                bm.indices.extend(indices_tmp)
+                tmp = np.swapaxes(bm.labelData, 0, 1)
+                tmp = np.ascontiguousarray(tmp)
+                indices_tmp = read_indices_allx(tmp, 1)
+                bm.indices.extend(indices_tmp)
+                tmp = np.swapaxes(tmp, 0, 2)
+                tmp = np.ascontiguousarray(tmp)
+                indices_tmp = read_indices_allx(tmp, 2)
+                bm.indices.extend(indices_tmp)
+
+                # labels must not be adjacent
+                neighbours = False
+                for k in range(3):
+                    sub_indices = [x for (x, y) in bm.indices if y == k]
+                    sub_indices_minus_one = [x - 1 for x in sub_indices]
+                    if any(i in sub_indices for i in sub_indices_minus_one):
+                        neighbours = True
+                if neighbours:
+                    bm = _error_(bm, 'At least one empty slice between labels required.')
+
+            # send executable
+            for dest in range(1, size):
+                comm.send(bm.success, dest=dest, tag=0)
+
+            if bm.success:
+
+                # When is domain decomposition faster?
+                bm = predict_blocksize(bm)
+                nbytes = (bm.argmax_z - bm.argmin_z) * (bm.argmax_y - bm.argmin_y) * (bm.argmax_x - bm.argmin_x) * 4
+
+                # small or large
+                if nbytes * bm.nol < 1e10 and nbytes < 2e9:
+
+                    # send "small" to childs
+                    for dest in range(1, size):
+                        comm.send(1, dest=dest, tag=1)
+
+                    # reduce blocksize
+                    bm.data = np.copy(bm.data[bm.argmin_z:bm.argmax_z, bm.argmin_y:bm.argmax_y, bm.argmin_x:bm.argmax_x], order='C')
+                    bm.labelData = np.copy(bm.labelData[bm.argmin_z:bm.argmax_z, bm.argmin_y:bm.argmax_y, bm.argmin_x:bm.argmax_x], order='C')
+
+                    # read labeled slices
+                    if bm.allaxis:
+                        bm.indices, bm.labels = [], []
+                        indices_tmp, labels_tmp = read_labeled_slices_allx(bm.labelData, 0)
+                        bm.indices.extend(indices_tmp)
+                        bm.labels.append(labels_tmp)
+                        tmp = np.swapaxes(bm.labelData, 0, 1)
+                        tmp = np.ascontiguousarray(tmp)
+                        indices_tmp, labels_tmp = read_labeled_slices_allx(tmp, 1)
+                        bm.indices.extend(indices_tmp)
+                        bm.labels.append(labels_tmp)
+                        tmp = np.swapaxes(tmp, 0, 2)
+                        tmp = np.ascontiguousarray(tmp)
+                        indices_tmp, labels_tmp = read_labeled_slices_allx(tmp, 2)
+                        bm.indices.extend(indices_tmp)
+                        bm.labels.append(labels_tmp)
+                    else:
+                        bm.indices, bm.labels = read_labeled_slices(bm.labelData)
+
+                    # number of ngpus
+                    ngpus = min(len(bm.indices), size)
+
+                    # send number of GPUs to childs
+                    for dest in range(1, size):
+                        comm.send(ngpus, dest=dest, tag=2)
+
+                    # create subcommunicator
+                    sub_comm = MPI.Comm.Split(comm, 1, rank)
+
+                    from biomedisa.features.random_walk.rw_small import _diffusion_child
+                    results = _diffusion_child(sub_comm, bm)
+
+                else:
+
+                    # send "large" to childs
+                    for dest in range(1, size):
+                        comm.send(0, dest=dest, tag=1)
+
+                    # number of ngpus
+                    ngpus = min((bm.argmax_z - bm.argmin_z) // 100, size)
+                    ngpus = max(ngpus, 1)
+
+                    # send number of GPUs to childs
+                    for dest in range(1, size):
+                        comm.send(ngpus, dest=dest, tag=2)
+
+                    # create subcommunicator
+                    sub_comm = MPI.Comm.Split(comm, 1, rank)
+
+                    from biomedisa.features.random_walk.rw_large import _diffusion_child
+                    results = _diffusion_child(sub_comm, bm)
+
+                return results
+
+    else:
+
+        # check if executable
+        executable = comm.recv(source=0, tag=0)
+
+        if executable:
+
+            # get small or large
+            small = comm.recv(source=0, tag=1)
+
+            # get number of gpus
+            ngpus = comm.recv(source=0, tag=2)
+
+            # create sub communicator
+            if rank >= ngpus:
+                sub_comm = MPI.Comm.Split(comm, 0, rank)     # set process to idle
+            else:
+                sub_comm = MPI.Comm.Split(comm, 1, rank)
+
+                if small:
+                    from biomedisa.features.random_walk.rw_small import _diffusion_child
+                    _diffusion_child(sub_comm)
+                else:
+                    from biomedisa.features.random_walk.rw_large import _diffusion_child
+                    _diffusion_child(sub_comm)
+
+if __name__ == '__main__':
+
+    # initialize arguments
+    parser = argparse.ArgumentParser(description='Biomedisa interpolation.',
+             formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    # required arguments
+    parser.add_argument('path_to_data', type=str, metavar='PATH_TO_IMAGE',
+                        help='Location of image data')
+    parser.add_argument('path_to_labels', type=str, metavar='PATH_TO_LABELS',
+                        help='Location of label data')
+
+    # optional arguments
+    parser.add_argument('-v', '--version', action='version', version=f'{biomedisa.__version__}',
+                        help='Biomedisa version')
+    parser.add_argument('--nbrw', type=int, default=10,
+                        help='Number of random walks starting at each pre-segmented pixel')
+    parser.add_argument('--sorw', type=int, default=4000,
+                        help='Steps of a random walk')
+    parser.add_argument('--acwe', action='store_true', default=False,
+                        help='Post-processing with active contour')
+    parser.add_argument('--acwe_alpha', metavar='ALPHA', type=float, default=1.0,
+                        help='Pushing force of active contour')
+    parser.add_argument('--acwe_smooth', metavar='SMOOTH', type=int, default=1,
+                        help='Smoothing steps of active contour')
+    parser.add_argument('--acwe_steps', metavar='STEPS', type=int, default=3,
+                        help='Iterations of active contour')
+    parser.add_argument('-nc', '--no_compression', action='store_true', default=False,
+                        help='Disable compression of segmentation results')
+    parser.add_argument('-allx', '--allaxis', action='store_true', default=False,
+                        help='If pre-segmentation is not exlusively in xy-plane')
+    parser.add_argument('-d', '--denoise', action='store_true', default=False,
+                        help='Smooth/denoise image data before processing')
+    parser.add_argument('-u', '--uncertainty', action='store_true', default=False,
+                        help='Return uncertainty of segmentation result')
+    parser.add_argument('-i', '--ignore', type=str, default='none',
+                        help='Ignore specific label(s), e.g. 2,5,6')
+    parser.add_argument('-o', '--only', type=str, default='all',
+                        help='Segment only specific label(s), e.g. 1,3,5')
+    parser.add_argument('-s', '--smooth', nargs='?', type=int, const=100, default=0,
+                        help='Number of smoothing iterations for segmentation result')
+    parser.add_argument('-c','--clean', nargs='?', type=float, const=0.1, default=None,
+                        help='Remove outliers, e.g. 0.5 means that objects smaller than 50 percent of the size of the largest object will be removed')
+    parser.add_argument('-f','--fill', nargs='?', type=float, const=0.9, default=None,
+                        help='Fill holes, e.g. 0.5 means that all holes smaller than 50 percent of the entire label will be filled')
+    parser.add_argument('-p', '--platform', default=None,
+                        help='One of "cuda", "opencl_NVIDIA_GPU", "opencl_Intel_CPU"')
+    parser.add_argument('-rh','--return_hits', action='store_true', default=False,
+                        help='Return hits from each label. Only works for small image data')
+    parser.add_argument('-iid','--img_id', type=str, default=None,
+                        help='Image ID within django environment/browser version')
+    parser.add_argument('-lid','--label_id', type=str, default=None,
+                        help='Label ID within django environment/browser version')
+    parser.add_argument('-r','--remote', action='store_true', default=False,
+                        help='The interpolation is carried out on a remote server. Must be set up in config.py')
+    parser.add_argument('-q','--queue', type=int, default=0,
+                        help='Processing queue when using a remote server')
+    kwargs = vars(parser.parse_args())
+
+    # run interpolation
+    smart_interpolation(None, None, **kwargs)
+