biomedisa 2024.5.19__tar.gz → 2024.5.21__tar.gz

{biomedisa-2024.5.19 → biomedisa-2024.5.21}/PKG-INFO

@@ -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-2024.5.19 → biomedisa-2024.5.21}/README.md

@@ -1,45 +1,50 @@
-[![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
@@ -61,14 +66,17 @@ 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
@@ -99,16 +107,16 @@ 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
@@ -127,11 +135,11 @@ 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
@@ -144,7 +152,7 @@ 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
@@ -177,7 +185,7 @@ 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
@@ -190,7 +198,7 @@ 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)
@@ -201,46 +209,21 @@ 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:
 
@@ -254,7 +237,7 @@ 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-2024.5.19 → biomedisa-2024.5.21}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biomedisa"
-version = "2024.5.19"
+version = "2024.5.21"
 authors = [
   { name="Philipp Lösel"}, {email="philipp.loesel@anu.edu.au" },
 ]

{biomedisa-2024.5.19 → biomedisa-2024.5.21}/src/biomedisa/__init__.py

@@ -1,15 +1,11 @@
 import os
-import sys
 import subprocess
 
-# from source base directory
+# base directory
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 
-# pip base directory
-if not os.path.exists(os.path.join(BASE_DIR,'biomedisa_features')):
-    BASE_DIR = os.path.dirname(os.path.abspath(__file__))
-    # add BASE_DIR to PYTHONPATH for absolute imports
-    sys.path.append(BASE_DIR)
+# pip installation
+if not os.path.exists(os.path.join(BASE_DIR,'biomedisa/settings.py')):
 
     # metadata
     import importlib_metadata

{biomedisa-2024.5.19 → biomedisa-2024.5.21}/src/biomedisa/deeplearning.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -27,13 +27,11 @@
 ##                                                                      ##
 ##########################################################################
 
-import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-sys.path.append(BASE_DIR)
+import os
 import biomedisa
-import biomedisa_features.crop_helper as ch
-from biomedisa_features.keras_helper import *
-from biomedisa_features.biomedisa_helper import _error_, unique_file_path
+import biomedisa.features.crop_helper as ch
+from biomedisa.features.keras_helper import *
+from biomedisa.features.biomedisa_helper import _error_, unique_file_path
 from tensorflow.python.framework.errors_impl import ResourceExhaustedError
 import tensorflow as tf
 import numpy as np
@@ -121,7 +119,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             project = os.path.splitext(bm.shortfilename)[0]
 
             # path to model
-            bm.path_to_model = BASE_DIR + f'/private_storage/images/{bm.username}/{project}.h5'
+            bm.path_to_model = biomedisa.BASE_DIR + f'/private_storage/images/{bm.username}/{project}.h5'
             if not bm.remote:
                 bm.path_to_model = unique_file_path(bm.path_to_model)
 
@@ -129,7 +127,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             project = os.path.splitext(os.path.basename(bm.path_to_model))[0]
 
         # create pid object
-        from biomedisa_features.django_env import create_pid_object
+        from biomedisa.features.django_env import create_pid_object
         create_pid_object(os.getpid(), bm.remote, bm.queue, bm.img_id, (bm.path_to_model if bm.train else ''))
 
         # write in log file
@@ -319,7 +317,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
     # django environment
     if bm.django_env:
         from biomedisa_app.config import config
-        from biomedisa_features.django_env import post_processing
+        from biomedisa.features.django_env import post_processing
         validation=True if bm.validation_split or (bm.val_images is not None and bm.val_images[0] is not None) else False
         post_processing(bm.path_to_final, time_str, config['SERVER_ALIAS'], bm.remote, bm.queue,
             img_id=bm.img_id, label_id=bm.label_id, path_to_model=bm.path_to_model,
@@ -327,7 +325,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             train=bm.train, predict=bm.predict, validation=validation)
 
         # write in log file
-        path_to_time = BASE_DIR + '/log/time.txt'
+        path_to_time = biomedisa.BASE_DIR + '/log/time.txt'
         with open(path_to_time, 'a') as timefile:
             if predict:
                 message = 'Successfully segmented ' + bm.shortfilename
@@ -490,7 +488,7 @@ if __name__ == '__main__':
             reference_image_path = bm.path_to_images
         bm.username = os.path.basename(os.path.dirname(reference_image_path))
         bm.shortfilename = os.path.basename(reference_image_path)
-        bm.path_to_logfile = BASE_DIR + '/log/logfile.txt'
+        bm.path_to_logfile = biomedisa.BASE_DIR + '/log/logfile.txt'
     else:
         bm.django_env = False
 

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.21/src/biomedisa/features}/DataGenerator.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.21/src/biomedisa/features}/DataGeneratorCrop.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.21/src/biomedisa/features}/PredictDataGenerator.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.21/src/biomedisa/features}/PredictDataGeneratorCrop.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2022 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.21/src/biomedisa/features}/active_contour.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -27,13 +27,10 @@
 ##                                                                      ##
 ##########################################################################
 
-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 os
 import biomedisa
-from biomedisa_features.curvop_numba import curvop, evolution
-from biomedisa_features.biomedisa_helper import (unique_file_path, load_data, save_data,
+from biomedisa.features.curvop_numba import curvop, evolution
+from biomedisa.features.biomedisa_helper import (unique_file_path, load_data, save_data,
     pre_processing, img_to_uint8, silent_remove)
 import numpy as np
 import numba
@@ -143,7 +140,7 @@ def activeContour(data, labelData, alpha=1.0, smooth=1, steps=3,
     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'
+        bm.path_to_logfile = biomedisa.BASE_DIR + '/log/logfile.txt'
 
     # pre-processing
     bm = pre_processing(bm)
@@ -234,13 +231,13 @@ def refinement(bm):
 
 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:
+        with open(biomedisa.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 biomedisa.features.create_slices import create_slices
         from redis import Redis
         from rq import Queue
 
@@ -300,7 +297,7 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
 
     # get host information
     host = ''
-    host_base = BASE_DIR
+    host_base = biomedisa.BASE_DIR
     subhost, qsub_pid = None, None
     if 'REMOTE_QUEUE_HOST' in config:
         host = config['REMOTE_QUEUE_HOST']
@@ -313,8 +310,8 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
         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 = ['python3', host_base+'/biomedisa/features/active_contour.py']
+            cmd += [image.pic.path.replace(biomedisa.BASE_DIR,host_base), friend.pic.path.replace(biomedisa.BASE_DIR,host_base)]
             cmd += [f'-iid={image.id}', f'-fid={friend.id}', '-r']
 
             # command (append only on demand)
@@ -338,8 +335,8 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
 
             # 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))
+            success+=send_data_to_host(image.pic.path, host+':'+image.pic.path.replace(biomedisa.BASE_DIR,host_base))
+            success+=send_data_to_host(friend.pic.path, host+':'+friend.pic.path.replace(biomedisa.BASE_DIR,host_base))
 
             if success==0:
 
@@ -355,14 +352,14 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
                 subprocess.Popen(cmd).wait()
 
                 # config
-                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_4', BASE_DIR+'/log/config_4']).wait()
+                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_4', biomedisa.BASE_DIR+'/log/config_4']).wait()
 
                 if success==0:
-                    with open(BASE_DIR + '/log/config_4', 'r') as configfile:
+                    with open(biomedisa.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))
+                    path_to_acwe = unique_file_path(acwe_on_host.replace(host_base,biomedisa.BASE_DIR))
 
                     # get results
                     subprocess.Popen(['scp', host+':'+acwe_on_host, path_to_acwe]).wait()

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.21/src/biomedisa/features}/assd.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##