biomedisa 2024.5.19__py3-none-any.whl → 2024.5.21__py3-none-any.whl

{biomedisa-2024.5.19.dist-info → biomedisa-2024.5.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.19
+Version: 2024.5.21
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -14,48 +14,53 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 
-[![biomedisa](biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
+[![biomedisa](https://raw.githubusercontent.com/biomedisa/biomedisa/master/biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
 -----------
 - [Overview](#overview)
 - [Hardware Requirements](#hardware-requirements)
 - [Installation (command-line based)](#installation-command-line-based)
 - [Installation (browser based)](#installation-browser-based)
 - [Download Data](#download-data)
+- [Revisions](#revisions)
 - [Smart Interpolation](#smart-interpolation)
 - [Deep Learning](#deep-learning)
 - [Biomedisa Features](#biomedisa-features)
-- [Update Biomedisa](#update-biomedisa)
-- [Releases](#releases)
 - [Authors](#authors)
 - [FAQ](#faq)
 - [Citation](#citation)
 - [License](#license)
 
-# Overview
+## Overview
 Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large volumetric images, e.g. CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's semi-automated segmentation is based on a smart interpolation of sparsely pre-segmented slices, taking into account the complete underlying image data. In addition, Biomedisa enables deep learning for the fully automated segmentation of series of similar samples. It can be used in combination with segmentation tools such as Amira/Avizo, ImageJ/Fiji and 3D Slicer. If you are using Biomedisa or the data for your research please cite: Lösel, P.D. et al. [Introducing Biomedisa as an open-source online platform for biomedical image segmentation.](https://www.nature.com/articles/s41467-020-19303-w) *Nat. Commun.* **11**, 5577 (2020).
 
-# Hardware Requirements
+## Hardware Requirements
 + One or more NVIDIA GPUs with compute capability 3.0 or higher or an Intel CPU.
 
-# Installation (command-line based)
+## Installation (command-line based)
 + [Ubuntu 22.04 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_cli.md)
 + [Ubuntu 22.04 + OpenCL + CPU (smart interpolation only and very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_opencl_cpu_cli.md)
 + [Windows 10 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_cli.md)
 + [Windows 10 + OpenCL + GPU (easy to install but lacks features like allaxis, smoothing, uncertainty, optimized GPU memory usage)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_gpu_cli.md)
 + [Windows 10 + OpenCL + CPU (very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_cpu_cli.md)
 
-# Installation (browser based)
+## Installation (browser based)
 + [Ubuntu 22.04](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8.md)
 
-# Download Data
+## Download Data
 + Download the data from our [gallery](https://biomedisa.info/gallery/)
 
-# Smart Interpolation
+## Revisions
+2024.05.21
++ Pip is the preferred installation method
++ Commands, module names and imports have been changed to conform to the Pip standard
++ For versions <=2023.09.1 please check [README](https://github.com/biomedisa/biomedisa/blob/master/README/deprecated/README_2023.09.1.md)
+
+## Smart Interpolation
 + [Parameters and Examples](https://github.com/biomedisa/biomedisa/blob/master/README/smart_interpolation.md)
 
 #### Python example
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 from biomedisa.interpolation import smart_interpolation
 
 # load data
@@ -77,14 +82,17 @@ save_data('Downloads/final.trigonopterus.smooth.am', smooth_result, header=heade
 #### Command-line based
 ```
 python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif
+
+# if pre-segmentation is not exclusively in the XY plane
+python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif --allaxis
 ```
 
-# Deep Learning
+## Deep Learning
 + [Parameters and Examples](https://github.com/biomedisa/biomedisa/blob/master/README/deep_learning.md)
 
 #### Python example (training)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data
+from biomedisa.features.biomedisa_helper import load_data
 from biomedisa.deeplearning import deep_learning
 
 # load image data
@@ -115,16 +123,16 @@ deep_learning(img_data, label_data, train=True, batch_size=12,
 #### Command-line based (training)
 ```
 # start training with a batch size of 12
-python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs 12
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs=12
 
 # validation (optional)
-python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi C:\Users\%USERNAME%\Downloads\val_img -vl C:\Users\%USERNAME%\Downloads\val_labels
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi=C:\Users\%USERNAME%\Downloads\val_img -vl=C:\Users\%USERNAME%\Downloads\val_labels
 ```
 If running into ResourceExhaustedError due to out of memory (OOM), try to use smaller batch size.
 
 #### Python example (prediction)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 from biomedisa.deeplearning import deep_learning
 
 # load data
@@ -143,11 +151,11 @@ save_data('final.Head5.am', results['regular'], results['header'])
 python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p
 ```
 
-# Biomedisa Features
+## Biomedisa Features
 
 #### Load and save data (such as Amira Mesh, TIFF, NRRD, NIfTI or DICOM)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 
 # load data as numpy array
 # for DICOM, PNG files, or similar formats, 'path_to_data' must reference
@@ -160,7 +168,7 @@ save_data(path_to_data, data, header)
 
 #### Create STL mesh from segmentation (label values are saved as attributes)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 from biomedisa.mesh import get_voxel_spacing, save_mesh
 
 # load segmentation
@@ -193,7 +201,7 @@ python -m biomedisa.mesh <path_to_data>
 
 #### Resize data
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import img_resize
+from biomedisa.features.biomedisa_helper import img_resize
 
 # resize image data
 zsh, ysh, xsh = data.shape
@@ -206,7 +214,7 @@ label_data = img_resize(label_data, new_zsh, new_ysh, new_xsh, labels=True)
 
 #### Remove outliers and fill holes
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import clean, fill
+from biomedisa.features.biomedisa_helper import clean, fill
 
 # delete outliers smaller than 90% of the segment
 label_data = clean(label_data, 0.9)
@@ -217,46 +225,21 @@ label_data = fill(label_data, 0.9)
 
 #### Accuracy assessment
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import Dice_score, ASSD
+from biomedisa.features.biomedisa_helper import Dice_score, ASSD
 dice = Dice_score(ground_truth, result)
 assd = ASSD(ground_truth, result)
 ```
 
-# Update Biomedisa
-If you installed Biomedisa via Pip
-```
-pip install --upgrade biomedisa
-```
-If you used `git clone`, change to the Biomedisa directory and make a pull request
-```
-cd git/biomedisa
-git pull
-```
-
-If you installed the browser based version of Biomedisa (including MySQL database), you also need to update the database
-```
-python manage.py migrate
-```
-
-If you installed an [Apache Server](https://github.com/biomedisa/biomedisa/blob/master/README/APACHE_SERVER.md), you need to restart the server
-```
-sudo service apache2 restart
-```
-
-# Releases
-
-For the versions available, see the [list of releases](https://github.com/biomedisa/biomedisa/releases). 
-
-# Authors
+## Authors
 
 * **Philipp D. Lösel**
 
 See also the list of [contributors](https://github.com/biomedisa/biomedisa/blob/master/credits.md) who participated in this project.
 
-# FAQ
+## FAQ
 Frequently asked questions can be found at: https://biomedisa.info/faq/.
 
-# Citation
+## Citation
 
 If you use Biomedisa or the data, please cite the following paper:
 
@@ -270,7 +253,7 @@ If you use Biomedisa's Smart Interpolation, you can also cite the initial descri
 
 `Lösel, P. & Heuveline, V. Enhancing a diffusion algorithm for 4D image segmentation using local information. Proc. SPIE 9784, 97842L (2016).` https://doi.org/10.1117/12.2216202
 
-# License
+## License
 
 This project is covered under the **EUROPEAN UNION PUBLIC LICENCE v. 1.2 (EUPL)**.
 

biomedisa-2024.5.21.dist-info/RECORD

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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-2024.5.19.dist-info/RECORD

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