install and astra tomopy venv instructions

README.md

@@ -21,15 +21,17 @@ git clone https://github.com/gianthk/alrecon.git
 2. Navigate to the repository and create a virtual environment with all necessary dependencies:
 ```commandline
 cd alrecon
-conda env create --file alrecon.yml
-conda activate alrecon
+conda env create --file envs/alrecon-base.yml
+conda activate alrecon-base
 ```
 > [!NOTE]
-> If you already have a destination virtual environment for alrecon, you can install manually the requirements listed in file [alrecon.yml](alrecon.yml).
+> If you already have a destination virtual environment for alrecon, you can install manually the requirements listed in file [alrecon.yml](envs/alrecon-base.yml).
+
+> [!NOTE]
+> To use TomoPy with CUDA features, install TomoPy from conda following [these instructions](https://tomopy.readthedocs.io/en/stable/install.html).
 
 3. Build the `alrecon` app:
 ```commandline
-cd alrecon
 pip install -e .
 ```
 
@@ -64,10 +66,17 @@ You can take a look at [solara's documnetation](https://solara.dev/api) for more
 ## Integration with Google Sheets
 - `Alrecon` allows you to keep a consistent log of all reconstruction jobs on an online master Google spreadsheet.
 - The integration uses [gspread](https://docs.gspread.org/en/v5.12.0/), a Python API for Google Sheets.
-- You will need to setup your Google account, enable Google Sheets API, and create a Secret Key for accessing your online master. Follow [these instructions](https://www.youtube.com/watch?v=hyUw-koO2DA) to setup the integration with Google Sheets.
+- You will need to setup your Google Cloud account, enable [Google Sheets API](https://developers.google.com/sheets/api/guides/concepts), and create a Secret Key with read/write permission to your online master Google sheet. Follow [these instructions](https://www.youtube.com/watch?v=hyUw-koO2DA) to setup the integration with Google Sheets API.
 
 ## Use with [napari](https://napari.org/stable/)
-napari is a pure Python powerfull viewer for multi-dimensional images. Until now, alrecon supports napari only when [running the app through Jupyter](#run-al-recon-within-jupyter).
+[napari](https://napari.org/stable/) is a pure Python powerfull viewer for multi-dimensional images. Until now, alrecon supports napari only when [running the app through Jupyter](#run-al-recon-within-jupyter).
+
+## Setup [ImageJ](https://imagej.net/software/fiji/) launcher
+To launch [ImageJ](https://imagej.net/software/fiji/) from the alrecon web app follow these steps:
+1. Modify the path to your ImageJ executable in the alrecon general settings
+![alrecon imagej executable path setting](docs/pictures/alrecon_imagej.png)
+
+2. Copy the [FolderOpener_virtual.ijm](/imagej_macros/FolderOpener_virtual.ijm) ImageJ macro contained in `/alrecon/imagej_macros/` to the plugin folder of your ImageJ installation. On Linux this is something like `/opt/Fiji.app/macros/`.
 
 ## Acknowledgements
 This work was performed within the [BEATS](https://beats-sesame.eu/) project and has received funding from the EU’s H2020 framework programme for research and innovation under grant agreement n° [822535](https://cordis.europa.eu/project/id/822535).

alrecon/__init__.py

@@ -1,4 +1,4 @@
 """Al-recon. Everyone can reconstruct"""
 __title__ = "Al-recon"
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 __description__ = "Computed Tomography reconstruction web applicatoin. Built with solara."

envs/alrecon-astra.yml

@@ -0,0 +1,20 @@
+name: alrecon
+channels:
+  - conda-forge
+dependencies:
+  - python=3.8
+  - astra-toolbox::astra-toolbox
+  - tomopy
+  - plotly::plotly
+  - dxchange
+  - pandas
+  - tifffile
+  - pip
+  - pip:
+      - pypng
+      - matplotlib
+      - gspread
+      - gspread-dataframe
+      - oauth2client
+      - solara
+      - napari

alrecon.yml → envs/alrecon-base.yml

@@ -1,20 +1,17 @@
 name: alrecon
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - python>=3.8
   - tomopy
   - dxchange
   - pip
   - pip:
-      - numpy
       - pandas
       - tifffile
       - pypng
       - plotly
       - matplotlib
-      - numexpr
       - gspread
       - gspread-dataframe
       - oauth2client

envs/install_alrecon_in_tomopy_dev_env.md

@@ -0,0 +1,51 @@
+## the following commands were used to create a virtual environment for alrecon with full GPU functionalities using astra-toolbox and tomopy
+```commandline
+conda create --name tomopy python=3.8
+conda activate tomopy
+conda install -c astra-toolbox astra-toolbox
+conda install -c conda-forge tomopy
+conda install dxchange pandas tifffile
+conda install -c conda-forge dxchange pandas tifffile
+pip install pypng matplotlib gspread gspread-dataframe oauth2client
+pip install solara
+```
+
+---
+## the following is an attempt to install tomopy and alrecon in development mode in a virtual environment with the astra-toolbox
+
+### 1. clone the TomoPy GitHub repository
+### 2. create virtual env
+```commandline
+conda env create -f /tomopy/envs/linux-cuda.yml --name alrecon python=3.8
+conda activate alrecon
+```
+
+### 3. install astra-toolbox
+```commandline
+conda install -c astra-toolbox astra-toolbox
+```
+
+### 4. build TomoPy
+```commandline
+cd tomopy/
+pip install . --no-deps
+mkdir build
+cd build
+cmake .. -GNinja -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DCMAKE_INSTALL_LIBDIR=lib
+cmake --build .
+cmake --install .
+```
+
+### 5. Clone the alrecon GitHub repository
+### 6. Install the alrecon dependencies
+```commandline
+cd alrecon/
+conda install -c plotly plotly
+conda install pandas tifffile 
+pip install pypng matplotlib gspread gspread-dataframe oauth2client
+pip install solara
+```
+### 7. Build alrecon
+```commandline
+pip install -e .
+```

imagej_macros/FolderOpener_virtual.ijm

@@ -0,0 +1,5 @@
+filelist = getArgument()
+print("Importing .TIFF sequence:")
+print(filelist)
+run("Image Sequence...", "open=" + filelist + " sort use");
+print("Done.")

pyproject.toml

@@ -25,23 +25,17 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering",
     "Topic :: Utilities",
 ]
 requires-python = ">=3.8"
 dynamic = ["version", "description"]
 dependencies = [
+    "tomopy",
     "pathlib",
-#    "logging",
-#    "random",
-#    "time",
-#    "math",
-    "numpy",
     "solara",
     "plotly",
     "dxchange",
-    "tomopy",
     "pyyaml",
     "numpy",
     "tifffile",
@@ -50,6 +44,8 @@ dependencies = [
 
 [project.optional-dependencies]
 all = [
+    "pandas",
+    "astra-toolbox::astra-toolbox",
     "gspread",
     "gspread_dataframe",
     "oauth2client",