Merge pull request #121 from dkazanc/libraryci

Major Documentation update and some CI changes

.github/workflows/libtomophantom_conda_upload.yml

@@ -0,0 +1,43 @@
+name: libtomophantom_conda_upload
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-22.04
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository code
+        uses: actions/checkout@v4
+
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies with Conda
+        run: |
+          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
+          $CONDA/bin/conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive
+          $CONDA/bin/conda install -c conda-forge cmake
+          $CONDA/bin/conda update conda
+          $CONDA/bin/conda update conda-build
+          $CONDA/bin/conda list
+
+      - name: Decrypt a secret
+        run: ./.scripts/decrypt_secret.sh
+        env:
+          LARGE_SECRET_PASSPHRASE: ${{ secrets.LARGE_SECRET_PASSPHRASE }}
+
+      - name: Upload the tested package to conda cloud
+        run: |
+          chmod +x ./.scripts/conda_upload_lib.sh
+          ./.scripts/conda_upload_lib.sh

.github/workflows/tomophantom_conda_upload.yml

@@ -1,31 +1,31 @@
-name: tomohantom_conda_upload
+name: tomophantom_conda_upload
 
-on: [push]
+on:
+  push:
+    branches:
+      - master
 
 jobs:
   build-linux:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
       - name: Checkout repository code
-        uses: actions/checkout@v3
-        with:
-          ref: "master"
-          fetch-depth: 0
+        uses: actions/checkout@v4
 
-      # setup Python 3.9
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Install dependencies with Conda
         run: |
-          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
+          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client          
           $CONDA/bin/conda update conda
           $CONDA/bin/conda update conda-build
           $CONDA/bin/conda list

.scripts/conda_upload.sh

@@ -9,11 +9,11 @@ mkdir ~/conda-bld
 conda config --set anaconda_upload no
 export CONDA_BLD_PATH=~/conda-bld
 
-export CIL_VERSION=3.0
+export CIL_VERSION=3.0.1
 $CONDA/bin/conda build conda-recipe . -c httomo
 
 # upload packages to conda
-find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file
+find $CONDA_BLD_PATH/$OS -name '*.tar.bz2' | while read -r file
 do
     echo $file
     $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force

.scripts/conda_upload_lib.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+PKG_NAME=libtomophantom
+USER=httomo-team
+OS=linux-64
+CONDA_TOKEN=$(cat $HOME/.secrets/my_secret.json)
+
+mkdir ~/conda-bld
+conda config --set anaconda_upload no
+export CONDA_BLD_PATH=~/conda-bld
+
+export CIL_VERSION=3.0.1
+$CONDA/bin/conda build conda-recipe_library . -c httomo
+
+# upload packages to conda
+find $CONDA_BLD_PATH/$OS -name '*.tar.bz2' | while read -r file
+do
+    echo $file
+    $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force
+done

CHANGES.md

@@ -1,5 +1,11 @@
 # ChangeLog
 
+## v3.0.1 (2024.12)
+
+* Documentation has been updated in January 2025 with a lot of additional information, API links, tutorials, etc.
+* Docstrings of the modules were updated with the references to documentation. 
+
+
 ## v3.0 (2023.12)
 * Project reorganised into two parts: a library that is build as a shared object using Cmake and Ctypes bindings and pure Python part that can be 
 installed separately. 

Demos/2D/Model.py

@@ -16,7 +16,6 @@
 
 model = 4  # select a model number from the library file (Phantom2DLibrary)
 N_size = 512  # set the desired dimension of the phantom
-# one can specify an exact path to the parameters file
 path = os.path.dirname(tomophantom.__file__)
 path_library2D = os.path.join(path, "phantomlib", "Phantom2DLibrary.dat")
 
@@ -29,6 +28,7 @@
 plt.imshow(phantom_2D, vmin=0, vmax=1, cmap="BuPu")
 plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
 plt.title("{}" "{}".format("2D Phantom using model no.", model))
+plt.show()
 
 # %%
 # Parameters to generate a sinogram
@@ -51,110 +51,111 @@
 plt.imshow(sino_an, vmin=0, vmax=300, cmap="BuPu")
 plt.colorbar(ticks=[0, 150, 300], orientation="vertical")
 plt.title("{}" "{}".format("Analytical sinogram of model no.", model))
-# %%
-# generate numerical sinogram
-angles_num = int(0.5 * np.pi * N_size)
-# angles number
-angles = np.linspace(0.0, 179.9, angles_num, dtype="float32")
-P = int(np.sqrt(2) * N_size)  # detectors
-
-tic = timeit.default_timer()
-sino_num = TomoP2D.SinoNum(phantom_2D, P, angles)
-toc = timeit.default_timer()
-Run_time = toc - tic
-print("Numerical sinogram has been generated in {} seconds".format(Run_time))
-
-plt.figure()
-plt.rcParams.update({"font.size": 21})
-plt.imshow(sino_num, vmin=0, vmax=300, cmap="BuPu")
-plt.colorbar(ticks=[0, 150, 300], orientation="vertical")
-plt.title("{}" "{}".format("Numerical sinogram of model no.", model))
+plt.show()
+# # %%
+# # generate numerical sinogram
+# angles_num = int(0.5 * np.pi * N_size)
+# # angles number
+# angles = np.linspace(0.0, 179.9, angles_num, dtype="float32")
+# P = int(np.sqrt(2) * N_size)  # detectors
+
+# tic = timeit.default_timer()
+# sino_num = TomoP2D.SinoNum(phantom_2D, P, angles)
+# toc = timeit.default_timer()
+# Run_time = toc - tic
+# print("Numerical sinogram has been generated in {} seconds".format(Run_time))
 
 # plt.figure()
-# plt.imshow(abs(sino_an-sino_num), vmin=0, vmax=0.001, cmap="BuPu")
-# plt.colorbar(ticks=[0, 0.02, 0.05], orientation='vertical')
-# plt.title('Analytical vs Numerical singograms')
-# %%
-
-
-###################################################################
-from tomobar.methodsDIR import RecToolsDIR
-
-angles_rad = angles * (np.pi / 180.0)
-
-# get numerical sinogram (ASTRA-toolbox)
-Rectools = RecToolsDIR(
-    DetectorsDimH=P,  # DetectorsDimH # detector dimension (horizontal)
-    DetectorsDimV=None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
-    CenterRotOffset=0.0,  # Center of Rotation (CoR) scalar (for 3D case only)
-    AnglesVec=angles_rad,  # array of angles in radians
-    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
-    device_projector="cpu",
-)
-
-tic = timeit.default_timer()
-sino_num_ASTRA = Rectools.FORWPROJ(phantom_2D)  # generate numerical sino (Ax)
-toc = timeit.default_timer()
-Run_time = toc - tic
-print("Numerical (ASTRA) sinogram has been generated in {} seconds".format(Run_time))
-
-plt.figure()
-plt.rcParams.update({"font.size": 21})
-plt.imshow(sino_num_ASTRA, vmin=0, vmax=150, cmap="BuPu")
-plt.colorbar(ticks=[0, 150, 250], orientation="vertical")
-plt.title("{}" "{}".format("Numerical sinogram (ASTRA) of model no.", model))
-# %%
-print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print("Reconstructing analytical sinogram using Fourier Slice method")
-print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+# plt.rcParams.update({"font.size": 21})
+# plt.imshow(sino_num, vmin=0, vmax=300, cmap="BuPu")
+# plt.colorbar(ticks=[0, 150, 300], orientation="vertical")
+# plt.title("{}" "{}".format("Numerical sinogram of model no.", model))
+
+# # plt.figure()
+# # plt.imshow(abs(sino_an-sino_num), vmin=0, vmax=0.001, cmap="BuPu")
+# # plt.colorbar(ticks=[0, 0.02, 0.05], orientation='vertical')
+# # plt.title('Analytical vs Numerical singograms')
+# # %%
+
+
+# ###################################################################
+# from tomobar.methodsDIR import RecToolsDIR
+
+# angles_rad = angles * (np.pi / 180.0)
+
+# # get numerical sinogram (ASTRA-toolbox)
+# Rectools = RecToolsDIR(
+#     DetectorsDimH=P,  # DetectorsDimH # detector dimension (horizontal)
+#     DetectorsDimV=None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
+#     CenterRotOffset=0.0,  # Center of Rotation (CoR) scalar (for 3D case only)
+#     AnglesVec=angles_rad,  # array of angles in radians
+#     ObjSize=N_size,  # a scalar to define reconstructed object dimensions
+#     device_projector="cpu",
+# )
+
+# tic = timeit.default_timer()
+# sino_num_ASTRA = Rectools.FORWPROJ(phantom_2D)  # generate numerical sino (Ax)
+# toc = timeit.default_timer()
+# Run_time = toc - tic
+# print("Numerical (ASTRA) sinogram has been generated in {} seconds".format(Run_time))
 
-RecFourier = Rectools.FOURIER(sino_an, "linear")
+# plt.figure()
+# plt.rcParams.update({"font.size": 21})
+# plt.imshow(sino_num_ASTRA, vmin=0, vmax=150, cmap="BuPu")
+# plt.colorbar(ticks=[0, 150, 250], orientation="vertical")
+# plt.title("{}" "{}".format("Numerical sinogram (ASTRA) of model no.", model))
+# # %%
+# print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+# print("Reconstructing analytical sinogram using Fourier Slice method")
+# print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
 
-plt.figure()
-plt.imshow(RecFourier, vmin=0, vmax=1, cmap="BuPu")
-plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
-plt.title("Fourier slice reconstruction")
-# %%
-print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print("Reconstructing analytical sinogram using FBP (tomobar)...")
-print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-# x = Atools.backproj(sino_an) # generate backprojection (A'b)
+# RecFourier = Rectools.FOURIER(sino_an, "linear")
 
-plt.figure()
-plt.subplot(121)
-plt.imshow(sino_an, cmap="BuPu")
-plt.title("Analytical sinogram")
-plt.subplot(122)
-plt.imshow(sino_num_ASTRA, cmap="BuPu")
-plt.title("Numerical sinogram")
-plt.show()
-# calculate norm
-# rmse1 = np.linalg.norm(sino_an - sino_num_ASTRA)/np.linalg.norm(sino_num_ASTRA)
+# plt.figure()
+# plt.imshow(RecFourier, vmin=0, vmax=1, cmap="BuPu")
+# plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
+# plt.title("Fourier slice reconstruction")
+# # %%
+# print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+# print("Reconstructing analytical sinogram using FBP (tomobar)...")
+# print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+# # x = Atools.backproj(sino_an) # generate backprojection (A'b)
 
-print("Reconstructing analytical sinogram using FBP (astra TB)...")
-FBPrec1 = Rectools.FBP(sino_an)
-plt.figure()
-plt.imshow(FBPrec1, vmin=0, vmax=1, cmap="BuPu")
-plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
-plt.title("FBP Reconstructed Phantom (analyt)")
+# plt.figure()
+# plt.subplot(121)
+# plt.imshow(sino_an, cmap="BuPu")
+# plt.title("Analytical sinogram")
+# plt.subplot(122)
+# plt.imshow(sino_num_ASTRA, cmap="BuPu")
+# plt.title("Numerical sinogram")
+# plt.show()
+# # calculate norm
+# # rmse1 = np.linalg.norm(sino_an - sino_num_ASTRA)/np.linalg.norm(sino_num_ASTRA)
+
+# print("Reconstructing analytical sinogram using FBP (astra TB)...")
+# FBPrec1 = Rectools.FBP(sino_an)
+# plt.figure()
+# plt.imshow(FBPrec1, vmin=0, vmax=1, cmap="BuPu")
+# plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
+# plt.title("FBP Reconstructed Phantom (analyt)")
 
-print("Reconstructing numerical sinogram using FBP (astra TB)...")
-FBPrec2 = Rectools.FBP(sino_num_ASTRA)
+# print("Reconstructing numerical sinogram using FBP (astra TB)...")
+# FBPrec2 = Rectools.FBP(sino_num_ASTRA)
 
-plt.figure()
-plt.imshow(FBPrec2, vmin=0, vmax=1, cmap="BuPu")
-plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
-plt.title("FBP Reconstructed Phantom (numeric)")
+# plt.figure()
+# plt.imshow(FBPrec2, vmin=0, vmax=1, cmap="BuPu")
+# plt.colorbar(ticks=[0, 0.5, 1], orientation="vertical")
+# plt.title("FBP Reconstructed Phantom (numeric)")
 
-plt.figure()
-plt.imshow(abs(FBPrec1 - FBPrec2), vmin=0, vmax=0.05, cmap="BuPu")
-plt.colorbar(ticks=[0, 0.02, 0.05], orientation="vertical")
-plt.title("FBP rec differences")
-# rmse2 = np.linalg.norm(FBPrec1 - FBPrec2)/np.linalg.norm(FBPrec2)
-
-Qtools = QualityTools(phantom_2D, FBPrec1)
-RMSE_FBP1 = Qtools.rmse()
-Qtools = QualityTools(phantom_2D, FBPrec2)
-RMSE_FBP2 = Qtools.rmse()
-print("RMSE for FBP (analyt) {}".format(RMSE_FBP1))
-print("RMSE for FBP (numeric) {}".format(RMSE_FBP2))
+# plt.figure()
+# plt.imshow(abs(FBPrec1 - FBPrec2), vmin=0, vmax=0.05, cmap="BuPu")
+# plt.colorbar(ticks=[0, 0.02, 0.05], orientation="vertical")
+# plt.title("FBP rec differences")
+# # rmse2 = np.linalg.norm(FBPrec1 - FBPrec2)/np.linalg.norm(FBPrec2)
+
+# Qtools = QualityTools(phantom_2D, FBPrec1)
+# RMSE_FBP1 = Qtools.rmse()
+# Qtools = QualityTools(phantom_2D, FBPrec2)
+# RMSE_FBP2 = Qtools.rmse()
+# print("RMSE for FBP (analyt) {}".format(RMSE_FBP1))
+# print("RMSE for FBP (numeric) {}".format(RMSE_FBP2))

Demos/2D/Object2D.py

@@ -7,11 +7,6 @@
 Script to generate 2D/3D analytical objects and their sinograms
 Recursively adding objects and sinos one can build a required model
 
->>>>> Optional dependencies (reconstruction mainly): <<<<<
-1. ASTRA toolbox: conda install -c astra-toolbox astra-toolbox
-2. tomobar: conda install -c dkazanc tomobar
-or install from https://github.com/dkazanc/ToMoBAR
-
 @author: Daniil Kazantsev
 """
 import numpy as np