biomedisa 2024.5.16__py3-none-any.whl → 2024.5.18__py3-none-any.whl

{biomedisa-2024.5.16.dist-info → biomedisa-2024.5.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.16
+Version: 2024.5.18
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -55,13 +55,8 @@ Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source applica
 
 #### Python example
 ```python
-# change this line to your biomedisa directory
-path_to_biomedisa = '/home/<user>/git/biomedisa'
-
-import sys
-sys.path.append(path_to_biomedisa)
-from biomedisa_features.biomedisa_helper import load_data, save_data
-from biomedisa_features.biomedisa_interpolation import smart_interpolation
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.interpolation import smart_interpolation
 
 # load data
 img, _ = load_data('Downloads/trigonopterus.tif')
@@ -81,11 +76,7 @@ save_data('Downloads/final.trigonopterus.smooth.am', smooth_result, header=heade
 
 #### Command-line based
 ```
-# change to the features directory
-cd git/biomedisa/biomedisa_features/
-
-# start smart interpolation
-python biomedisa_interpolation.py C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif
+python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif
 ```
 
 # Deep Learning
@@ -93,14 +84,8 @@ python biomedisa_interpolation.py C:\Users\%USERNAME%\Downloads\tumor.tif C:\Use
 
 #### Python example (training)
 ```python
-# change this line to your biomedisa directory
-path_to_biomedisa = '/home/<user>/git/biomedisa'
-
-# load libraries
-import sys
-sys.path.append(path_to_biomedisa)
-from biomedisa_features.biomedisa_helper import load_data
-from biomedisa_features.biomedisa_deeplearning import deep_learning
+from biomedisa.biomedisa_features.biomedisa_helper import load_data
+from biomedisa.deeplearning import deep_learning
 
 # load image data
 img1, _ = load_data('Head1.am')
@@ -129,27 +114,18 @@ deep_learning(img_data, label_data, train=True, batch_size=12,
 
 #### Command-line based (training)
 ```
-# change to the features directory
-cd git/biomedisa/biomedisa_features/
-
 # start training with a batch size of 12
-python biomedisa_deeplearning.py 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 biomedisa_deeplearning.py 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
-# change this line to your biomedisa directory
-path_to_biomedisa = '/home/<user>/git/biomedisa'
-
-# load libraries
-import sys
-sys.path.append(path_to_biomedisa)
-from biomedisa_features.biomedisa_helper import load_data, save_data
-from biomedisa_features.biomedisa_deeplearning import deep_learning
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.deeplearning import deep_learning
 
 # load data
 img, _ = load_data('Head5.am')
@@ -164,20 +140,15 @@ save_data('final.Head5.am', results['regular'], results['header'])
 
 #### Command-line based (prediction)
 ```
-# change to the features directory
-cd git/biomedisa/biomedisa_features/
-
 # start prediction with a batch size of 6
-python biomedisa_deeplearning.py C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p -bs 6
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p -bs 6
 ```
 
 # Biomedisa Features
 
 #### Load and save data (such as Amira Mesh, TIFF, NRRD, NIfTI or DICOM)
 ```python
-import sys
-sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
-from biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.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
@@ -190,10 +161,8 @@ save_data(path_to_data, data, header)
 
 #### Create STL mesh from segmentation (label values are saved as attributes)
 ```python
-import os, sys
-sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
-from biomedisa_features.biomedisa_helper import load_data, save_data
-from biomedisa_features.create_mesh import get_voxel_spacing, save_mesh
+from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.mesh import get_voxel_spacing, save_mesh
 
 # load segmentation
 data, header, extension = load_data(path_to_data, return_extension=True)
@@ -209,7 +178,7 @@ save_mesh(path_to_data, data, x_res, y_res, z_res, poly_reduction=0.9, smoothing
 
 #### Create mesh directly
 ```
-python git/biomedisa/biomedisa_features/create_mesh.py <path_to_data>
+python -m biomedisa.mesh <path_to_data>
 ```
 
 #### Options
@@ -225,9 +194,7 @@ python git/biomedisa/biomedisa_features/create_mesh.py <path_to_data>
 
 #### Resize data
 ```python
-import os, sys
-sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
-from biomedisa_features.biomedisa_helper import img_resize
+from biomedisa.biomedisa_features.biomedisa_helper import img_resize
 
 # resize image data
 zsh, ysh, xsh = data.shape
@@ -240,7 +207,7 @@ label_data = img_resize(label_data, new_zsh, new_ysh, new_xsh, labels=True)
 
 #### Remove outliers and fill holes
 ```python
-from biomedisa_features.biomedisa_helper import clean, fill
+from biomedisa.biomedisa_features.biomedisa_helper import clean, fill
 
 # delete outliers smaller than 90% of the segment
 label_data = clean(label_data, 0.9)
@@ -251,24 +218,28 @@ label_data = fill(label_data, 0.9)
 
 #### Accuracy assessment
 ```python
-from biomedisa_features.biomedisa_helper import Dice_score, ASSD
+from biomedisa.biomedisa_features.biomedisa_helper import Dice_score, ASSD
 dice = Dice_score(ground_truth, result)
 assd = ASSD(ground_truth, result)
 ```
 
 # Update Biomedisa
-If you have used `git clone`, change to the Biomedisa directory and make a pull request.
+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 have installed the browser based version of Biomedisa (including MySQL database), you also need to update the database.
+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 have installed an [Apache Server](https://github.com/biomedisa/biomedisa/blob/master/README/APACHE_SERVER.md), you need to restart the server.
+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
 ```

{biomedisa-2024.5.16.dist-info → biomedisa-2024.5.18.dist-info}/RECORD

@@ -37,8 +37,8 @@ biomedisa/biomedisa_features/random_walk/pyopencl_large.py,sha256=cOBhvxrdKCkbr6
 biomedisa/biomedisa_features/random_walk/pyopencl_small.py,sha256=2XALYNNv9D8Gb1u2lcjR1O4W9UM0Xxjj0r4nr-NiEkk,17068
 biomedisa/biomedisa_features/random_walk/rw_large.py,sha256=FERIsTXmqZprGCTShRR75PesIX5MMVtptk-SqI-4abo,19805
 biomedisa/biomedisa_features/random_walk/rw_small.py,sha256=0YFL0Ovb_400Ikbxv5yOXWskl3vAyfQ_0_Gz5EXzvVQ,14881
-biomedisa-2024.5.16.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
-biomedisa-2024.5.16.dist-info/METADATA,sha256=h2Eq4HFLRDvAG4P-TgLp1FgQkq6_p50v1pYxtSCSA7k,11677
-biomedisa-2024.5.16.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-biomedisa-2024.5.16.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
-biomedisa-2024.5.16.dist-info/RECORD,,
+biomedisa-2024.5.18.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-2024.5.18.dist-info/METADATA,sha256=Ck2qVtPA2ayKHrT0Rq7MUKl9wSWlvp9XNKxQ5HsTsHU,10748
+biomedisa-2024.5.18.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+biomedisa-2024.5.18.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-2024.5.18.dist-info/RECORD,,