biomedisa 2024.5.14__py3-none-any.whl

biomedisa/biomedisa_features/active_contour.py

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+#!/usr/bin/python3
+##########################################################################
+##                                                                      ##
+##  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__)))
+if not BASE_DIR in sys.path:
+    sys.path.append(BASE_DIR)
+import biomedisa
+from biomedisa_features.curvop_numba import curvop, evolution
+from biomedisa_features.biomedisa_helper import (load_data, save_data,
+    pre_processing, img_to_uint8, silent_remove)
+import numpy as np
+import numba
+import argparse
+import traceback
+import subprocess
+
+class Biomedisa(object):
+     pass
+
+@numba.jit(nopython=True)
+def geodis(c,sqrt2,sqrt3,iterations):
+    zsh, ysh, xsh = c.shape
+    for i in range(iterations):
+        for z in range(1,zsh):
+            for y in range(1,ysh-1):
+                for x in range(1,xsh-1):
+                    a1 = c[z-1,y-1,x-1] + sqrt3
+                    a2 = c[z-1,y-1,x] + sqrt2
+                    a3 = c[z-1,y-1,x+1] + sqrt3
+                    a4 = c[z-1,y,x-1] + sqrt2
+                    a5 = c[z-1,y,x] + 1
+                    a6 = c[z-1,y,x+1] + sqrt2
+                    a7 = c[z-1,y+1,x-1] + sqrt3
+                    a8 = c[z-1,y+1,x] + sqrt2
+                    a9 = c[z-1,y+1,x+1] + sqrt3
+                    a10 = c[z,y-1,x-1] + sqrt2
+                    a11 = c[z,y-1,x] + 1
+                    a12 = c[z,y-1,x+1] + sqrt2
+                    a13 = c[z,y,x-1] + 1
+                    a14 = c[z,y,x]
+                    c[z,y,x] = min(a1,a2,a3,a4,a5,a6,a7,a8,a9,a10,a11,a12,a13,a14)
+        for z in range(zsh-2,-1,-1):
+            for y in range(ysh-2,0,-1):
+                for x in range(xsh-2,0,-1):
+                    a1 = c[z+1,y-1,x-1] + sqrt3
+                    a2 = c[z+1,y-1,x] + sqrt2
+                    a3 = c[z+1,y-1,x+1] + sqrt3
+                    a4 = c[z+1,y,x-1] + sqrt2
+                    a5 = c[z+1,y,x] + 1
+                    a6 = c[z+1,y,x+1] + sqrt2
+                    a7 = c[z+1,y+1,x-1] + sqrt3
+                    a8 = c[z+1,y+1,x] + sqrt2
+                    a9 = c[z+1,y+1,x+1] + sqrt3
+                    a10 = c[z,y+1,x+1] + sqrt2
+                    a11 = c[z,y+1,x] + 1
+                    a12 = c[z,y+1,x-1] + sqrt2
+                    a13 = c[z,y,x+1] + 1
+                    a14 = c[z,y,x]
+                    c[z,y,x] = min(a1,a2,a3,a4,a5,a6,a7,a8,a9,a10,a11,a12,a13,a14)
+    return c
+
+def reduce_blocksize(raw, slices):
+    zsh, ysh, xsh = slices.shape
+    argmin_z, argmax_z, argmin_y, argmax_y, argmin_x, argmax_x = zsh, 0, ysh, 0, xsh, 0
+    for k in range(zsh):
+        y, x = np.nonzero(slices[k])
+        if x.any():
+            argmin_x = min(argmin_x, np.amin(x))
+            argmax_x = max(argmax_x, np.amax(x))
+            argmin_y = min(argmin_y, np.amin(y))
+            argmax_y = max(argmax_y, np.amax(y))
+            argmin_z = min(argmin_z, k)
+            argmax_z = max(argmax_z, k)
+    argmin_x = argmin_x - 100 if argmin_x - 100 > 0 else 0
+    argmax_x = argmax_x + 100 if argmax_x + 100 < xsh else xsh
+    argmin_y = argmin_y - 100 if argmin_y - 100 > 0 else 0
+    argmax_y = argmax_y + 100 if argmax_y + 100 < ysh else ysh
+    argmin_z = argmin_z - 100 if argmin_z - 100 > 0 else 0
+    argmax_z = argmax_z + 100 if argmax_z + 100 < zsh else zsh
+    raw = raw[argmin_z:argmax_z, argmin_y:argmax_y, argmin_x:argmax_x]
+    slices = slices[argmin_z:argmax_z, argmin_y:argmax_y, argmin_x:argmax_x]
+    return raw, slices, argmin_z, argmax_z, argmin_y, argmax_y, argmin_x, argmax_x
+
+def activeContour(data, labelData, alpha=1.0, smooth=1, steps=3,
+    path_to_data=None, path_to_labels=None, no_compression=False,
+    ignore='none', only='all', simple=False,
+    img_id=None, friend_id=None, remote=False):
+
+    # create biomedisa
+    bm = Biomedisa()
+    bm.process = 'acwe'
+    bm.success = True
+
+    # 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 bm.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
+
+    if bm.django_env:
+        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 = BASE_DIR + '/log/logfile.txt'
+
+    # pre-processing
+    bm = pre_processing(bm)
+
+    # create path_to_acwe
+    if bm.path_to_data:
+        filename, extension = os.path.splitext(bm.path_to_labels)
+        if extension == '.gz':
+            filename = filename[:-4]
+        suffix='.refined' if simple else '.acwe'
+        path_to_acwe = filename + suffix + bm.final_image_type
+
+    if bm.success:
+
+        # data type
+        bm.data = img_to_uint8(bm.data)
+
+        # append data
+        zsh, ysh, xsh = bm.data.shape
+        tmp = np.zeros((2+zsh, 2+ysh, 2+xsh), dtype=bm.data.dtype)
+        tmp[1:-1,1:-1,1:-1] = bm.data
+        bm.data = np.copy(tmp, order='C')
+        tmp = np.zeros((2+zsh, 2+ysh, 2+xsh), dtype=bm.labelData.dtype)
+        tmp[1:-1,1:-1,1:-1] = bm.labelData
+        bm.labelData = np.copy(tmp, order='C')
+        zsh, ysh, xsh = bm.data.shape
+
+        # reduce blocksize
+        bm.data, bm.labelData, argmin_z, argmax_z, argmin_y, argmax_y, argmin_x, argmax_x = reduce_blocksize(bm.data, bm.labelData)
+        bm.labelData = np.copy(bm.labelData, order='C')
+        bm.data = np.copy(bm.data, order='C')
+
+        # active contour
+        if simple:
+            bm.labelData = refinement(bm)
+        else:
+            for n in range(bm.steps):
+                print('Step:', n+1, '/', bm.steps)
+                mean = np.zeros(256, dtype=np.float32)
+                for k in bm.allLabels:
+                    inside = bm.labelData==k
+                    if np.any(inside):
+                        mean[k] = np.mean(bm.data[inside])
+                bm.labelData = evolution(mean, bm.labelData, bm.data, bm.alpha)
+                for k in bm.allLabels:
+                    bm.labelData = curvop(bm.labelData, bm.smooth, k, bm.allLabels)
+
+        # return to original data size
+        final = np.zeros((zsh, ysh, xsh), dtype=np.uint8)
+        final[argmin_z:argmax_z, argmin_y:argmax_y, argmin_x:argmax_x] = bm.labelData
+        final = np.copy(final[1:-1, 1:-1, 1:-1], order='C')
+
+        # save result
+        if bm.django_env and not bm.remote:
+            from biomedisa_app.views import unique_file_path
+            path_to_acwe = unique_file_path(path_to_acwe)
+        if bm.path_to_data:
+            save_data(path_to_acwe, final, bm.header, bm.final_image_type, bm.compression)
+
+        # post processing
+        if bm.django_env:
+            post_processing(path_to_acwe, bm.img_id, bm.friend_id, bm.simple, bm.remote)
+
+        return final
+
+def refinement(bm):
+    zsh, ysh, xsh = bm.data.shape
+    distance = np.zeros(bm.data.shape, dtype=np.float32)
+    distance[bm.labelData==0] = 100
+    distance = geodis(distance,np.sqrt(2),np.sqrt(3),1)
+    distance[distance<=10] = 0
+    distance[distance>10] = 1
+    distance = distance.astype(np.uint8)
+    result = np.zeros_like(bm.labelData)
+    for l in bm.allLabels[1:]:
+        for k in range(zsh):
+            img = bm.data[k]
+            mask = bm.labelData[k]
+            d = distance[k]
+            if np.any(np.logical_and(d==0,mask==l)) and np.any(np.logical_and(d==0,mask!=l)):
+                m1,s1 = np.mean(img[np.logical_and(d==0,mask==l)]), np.std(img[np.logical_and(d==0,mask==l)])
+                m2,s2 = np.mean(img[np.logical_and(d==0,mask!=l)]), np.std(img[np.logical_and(d==0,mask!=l)])
+                s1 = max(s1,1)
+                s2 = max(s2,1)
+                p1 = np.exp(-(img-m1)**2/(2*s1**2))/np.sqrt(2*np.pi*s1**2)
+                p2 = np.exp(-(img-m2)**2/(2*s2**2))/np.sqrt(2*np.pi*s2**2)
+                result[k] = np.logical_and(d==0, p1 > p2) * l
+    return result
+
+def post_processing(path_to_acwe, image_id=None, friend_id=None, simple=False, remote=False):
+    if remote:
+        with open(BASE_DIR + '/log/config_4', 'w') as configfile:
+            print(path_to_acwe, 'phantom', file=configfile)
+    else:
+        import django
+        django.setup()
+        from biomedisa_app.models import Upload
+        from biomedisa_features.create_slices import create_slices
+        from redis import Redis
+        from rq import Queue
+
+        # check if reference data still exists
+        image = Upload.objects.filter(pk=image_id)
+        friend = Upload.objects.filter(pk=friend_id)
+        if len(friend)>0:
+            friend = friend[0]
+
+            # create django object
+            shortfilename = os.path.basename(path_to_acwe)
+            pic_path = 'images/' + friend.user.username + '/' + shortfilename
+            Upload.objects.create(pic=pic_path, user=friend.user, project=friend.project, final=(10 if simple else 3), imageType=3, shortfilename=shortfilename, friend=friend_id)
+
+            # create slices
+            if len(image)>0:
+                q = Queue('slices', connection=Redis())
+                job = q.enqueue_call(create_slices, args=(image[0].pic.path, path_to_acwe,), timeout=-1)
+        else:
+            silent_remove(path_to_acwe)
+
+def init_active_contour(image_id, friend_id, label_id, simple=False):
+    '''
+    Runs activeContour() within django environment/webbrowser version
+
+    Parameters
+    ---------
+    image_id: int
+        Django id of image data
+    friend_id: int
+        Django id of result data to be processed
+    label_id: int
+        Django id of label data used for configuration parameters
+    simple: bool
+        Use simplified version of active contour
+
+    Returns
+    -------
+    No returns
+        Fails silently
+    '''
+
+    import django
+    django.setup()
+    from biomedisa_app.models import Upload
+    from biomedisa_app.config import config
+    from biomedisa_app.views import send_data_to_host, qsub_start, qsub_stop, unique_file_path
+
+    # get objects
+    try:
+        image = Upload.objects.get(pk=image_id)
+        label = Upload.objects.get(pk=label_id)
+        friend = Upload.objects.get(pk=friend_id)
+        success = True
+    except Upload.DoesNotExist:
+        success = False
+
+    # get host information
+    host = ''
+    host_base = BASE_DIR
+    subhost, qsub_pid = None, None
+    if 'REMOTE_QUEUE_HOST' in config:
+        host = config['REMOTE_QUEUE_HOST']
+    if host and 'REMOTE_QUEUE_BASE_DIR' in config:
+        host_base = config['REMOTE_QUEUE_BASE_DIR']
+
+    if success:
+
+        # remote server
+        if host:
+
+            # command
+            cmd = ['python3', host_base+'/biomedisa_features/active_contour.py']
+            cmd += [image.pic.path.replace(BASE_DIR,host_base), friend.pic.path.replace(BASE_DIR,host_base)]
+            cmd += [f'-iid={image.id}', f'-fid={friend.id}', '-r']
+
+            # command (append only on demand)
+            if simple:
+                cmd += ['-si']
+            if not label.compression:
+                cmd += ['-nc']
+            if label.ignore != 'none':
+                cmd += [f'-i={label.ignore}']
+            if label.only != 'all':
+                cmd += [f'-o={label.only}']
+            if label.ac_smooth != 1:
+                cmd += [f'-s={label.ac_smooth}']
+            if label.ac_steps != 3:
+                cmd += [f'-st={label.ac_steps}']
+            if label.ac_alpha != 1.0:
+                cmd += [f'-a={label.ac_alpha}']
+
+            # create user directory
+            subprocess.Popen(['ssh', host, 'mkdir', '-p', host_base+'/private_storage/images/'+image.user.username]).wait()
+
+            # send data to host
+            success=0
+            success+=send_data_to_host(image.pic.path, host+':'+image.pic.path.replace(BASE_DIR,host_base))
+            success+=send_data_to_host(friend.pic.path, host+':'+friend.pic.path.replace(BASE_DIR,host_base))
+
+            if success==0:
+
+                # qsub start
+                if 'REMOTE_QUEUE_QSUB' in config and config['REMOTE_QUEUE_QSUB']:
+                    subhost, qsub_pid = qsub_start(host, host_base, 4)
+
+                # start active contour
+                if subhost:
+                    cmd = ['ssh', '-t', host, 'ssh', subhost] + cmd
+                else:
+                    cmd = ['ssh', host] + cmd
+                subprocess.Popen(cmd).wait()
+
+                # config
+                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_4', BASE_DIR+'/log/config_4']).wait()
+
+                if success==0:
+                    with open(BASE_DIR + '/log/config_4', 'r') as configfile:
+                        acwe_on_host, _ = configfile.read().split()
+
+                    # local file names
+                    path_to_acwe = unique_file_path(acwe_on_host.replace(host_base,BASE_DIR))
+
+                    # get results
+                    subprocess.Popen(['scp', host+':'+acwe_on_host, path_to_acwe]).wait()
+
+                    # post processing
+                    post_processing(path_to_acwe, image_id=image_id, friend_id=friend_id, simple=simple)
+
+                    # remove config file
+                    subprocess.Popen(['ssh', host, 'rm', host_base + '/log/config_4']).wait()
+
+        # local server
+        else:
+            try:
+                activeContour(None, None, path_to_data=image.pic.path, path_to_labels=friend.pic.path,
+                    alpha=label.ac_alpha, smooth=label.ac_smooth, steps=label.ac_steps,
+                    no_compression=(False if label.compression else True),
+                    simple=simple, img_id=image_id, friend_id=friend_id, remote=False)
+            except Exception as e:
+                print(traceback.format_exc())
+
+    # qsub stop
+    if 'REMOTE_QUEUE_QSUB' in config and config['REMOTE_QUEUE_QSUB']:
+        qsub_stop(host, host_base, 4, 'acwe', subhost, qsub_pid)
+
+if __name__ == '__main__':
+
+    # initialize arguments
+    parser = argparse.ArgumentParser(description='Biomedisa active contour.',
+             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('-si','--simple', action='store_true', default=False,
+                        help='Simplified version of active contour')
+    parser.add_argument('-a', '--alpha', type=float, default=1.0,
+                        help='Driving force of contour')
+    parser.add_argument('-s', '--smooth', type=int, default=1,
+                        help='Number of smoothing steps')
+    parser.add_argument('-st', '--steps', type=int, default=3,
+                        help='Number of iterations')
+    parser.add_argument('-nc', '--no_compression', action='store_true', default=False,
+                        help='Disable compression of segmentation results')
+    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('-iid','--img_id', type=str, default=None,
+                        help='Image ID within django environment/browser version')
+    parser.add_argument('-fid','--friend_id', type=str, default=None,
+                        help='Label ID within django environment/browser version')
+    parser.add_argument('-r','--remote', action='store_true', default=False,
+                        help='Process is carried out on a remote server. Must be set up in config.py')
+
+    kwargs = vars(parser.parse_args())
+
+    # run active contour
+    try:
+        activeContour(None, None, **kwargs)
+    except Exception as e:
+        print(traceback.format_exc())
+