From ef3ffd85f527b0de9f0cffd6b43a6688ac6c0543 Mon Sep 17 00:00:00 2001 From: Thomas Athey Date: Tue, 23 May 2023 08:28:32 -0500 Subject: [PATCH 1/5] update readme --- docs/notebooks/pipelines/BrainLine/README.md | 22 +++++++++++-------- .../pipelines/BrainLine/soma_analysis.ipynb | 2 +- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/docs/notebooks/pipelines/BrainLine/README.md b/docs/notebooks/pipelines/BrainLine/README.md index dd0fa69e2..01cb8a0fe 100644 --- a/docs/notebooks/pipelines/BrainLine/README.md +++ b/docs/notebooks/pipelines/BrainLine/README.md @@ -1,12 +1,16 @@ -1. Install [Python 3.8](https://www.python.org/downloads/) -2. Install virtualenv `pip install virtualenv` -3. Make virtual environment ` -m virtualenv ` -4. Activate virtual environment e.g. `source /bin/activate` -5. Clone the repository `git clone https://github.com/neurodata/brainlit.git` -5. Install brainlit `pip install brainlit` or `cd brainlit && pip install -e .` -6. Install [ilastik](https://www.ilastik.org/) -7. Setup jupyter notebooks either by installing [VSCode](https://code.visualstudio.com/download) or [Jupyter Notebooks](https://jupyter.org/install) -8. Run the `soma_analysis.ipynb` or `axon_analysis.ipynb` +TACC Tutorial +------------- +1. In home directory (`cdh`) make python 3.9 virtual environment: `python3 -m venv venv_39`. +2. Activate virtual environment: `source venv_39/bin/activate`. +3. In scratch directory (`cds`), download ilastik (`wget https://files.ilastik.org/ilastik-1.4.0-Linux.tar.bz2`). +4. Decompress the ilastik file (`tar –xvzf ilastik-1.4.0-Linux.tar.bz2`). +5. Clone brainlit repository (`git clone https://github.com/neurodata/brainlit.git`). +6. Install brainlit from source in editable mode: `cd brainlit && pip install -e .`. +7. Install packages I use for this tutorial: `pip install matplotlib-scalebar jupyter`. +8. Go back to the home directory (`cdh`) and copy the notebook I made: `cp /home1/09423/tathey1/brainline-tacc-tutorial.ipynb .`. +9. Create jupyter kernel for this virtual environment: `ipython kernel install --name "venv_39" --user`. +10. Open the jupyter notebook and select `venv_39` as the kernel. +11. As you run the notebook, you will need to change a couple variables including `brainlit_path` and `ilastik_path` according to your scratch directory path. Atlas diff --git a/docs/notebooks/pipelines/BrainLine/soma_analysis.ipynb b/docs/notebooks/pipelines/BrainLine/soma_analysis.ipynb index 5f0bf35e8..e366c1502 100644 --- a/docs/notebooks/pipelines/BrainLine/soma_analysis.ipynb +++ b/docs/notebooks/pipelines/BrainLine/soma_analysis.ipynb @@ -552,7 +552,7 @@ "metadata": {}, "source": [ "```\n", - "python -m cloudreg.scripts.registration -input_s3_path precomputed://s3://smartspim-precomputed-volumes/2022_02_02/8604/Ch_561 --output_s3_path precomputed://s3://smartspim-precomputed-volumes/2022_02_02/8604/atlas_to_target --atlas_s3_path https://open-neurodata.s3.amazonaws.com/ara_2016/sagittal_50um/average_50um --parcellation_s3_path https://open-neurodata.s3.amazonaws.com/ara_2016/sagittal_10um/annotation_10um_2017 --atlas_orientation PIR -orientation ARS --rotation 0 0 0 --translation 0 0 0 --fixed_scale .7 -log_s3_path precomputed://s3://smartspim-precomputed-volumes/2022_02_02/8604/atlas_to_target --missing_data_correction True --grid_correction False --bias_correction True --regularization 5000.0 --iterations 3000 --registration_resolution 100\n", + "python -m cloudreg.scripts.registration -input_s3_path precomputed://s3://smartspim-precomputed-volumes/2023_04_13/MS36/Ch_561 --output_s3_path precomputed://s3://smartspim-precomputed-volumes/2023_04_13/MS36/atlas_to_target --atlas_s3_path https://open-neurodata.s3.amazonaws.com/ara_2016/sagittal_50um/average_50um --parcellation_s3_path https://open-neurodata.s3.amazonaws.com/ara_2016/sagittal_10um/annotation_10um_2017 --atlas_orientation PIR -orientation RPI --rotation 0 0 0 --translation 0 0 0 --fixed_scale 1 -log_s3_path precomputed://s3://smartspim-precomputed-volumes/2023_04_13/MS36/atlas_to_target --missing_data_correction True --grid_correction False --bias_correction True --regularization 5000.0 --iterations 3000 --registration_resolution 100\n", "```" ] }, From 3b27fb605258da1ebdd0105a8cc5e6302b5c42ae Mon Sep 17 00:00:00 2001 From: Thomas Athey Date: Tue, 23 May 2023 08:50:41 -0500 Subject: [PATCH 2/5] return --- docs/notebooks/pipelines/BrainLine/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/notebooks/pipelines/BrainLine/README.md b/docs/notebooks/pipelines/BrainLine/README.md index 01cb8a0fe..7dc0fac9b 100644 --- a/docs/notebooks/pipelines/BrainLine/README.md +++ b/docs/notebooks/pipelines/BrainLine/README.md @@ -1,5 +1,6 @@ TACC Tutorial ------------- + 1. In home directory (`cdh`) make python 3.9 virtual environment: `python3 -m venv venv_39`. 2. Activate virtual environment: `source venv_39/bin/activate`. 3. In scratch directory (`cds`), download ilastik (`wget https://files.ilastik.org/ilastik-1.4.0-Linux.tar.bz2`). From 75c8e30db75e3b86e3695068e1168afda5a5d426 Mon Sep 17 00:00:00 2001 From: Thomas Athey Date: Tue, 23 May 2023 10:54:59 -0400 Subject: [PATCH 3/5] Update README.md --- docs/notebooks/pipelines/BrainLine/README.md | 21 ++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/docs/notebooks/pipelines/BrainLine/README.md b/docs/notebooks/pipelines/BrainLine/README.md index 7dc0fac9b..823e3160d 100644 --- a/docs/notebooks/pipelines/BrainLine/README.md +++ b/docs/notebooks/pipelines/BrainLine/README.md @@ -3,18 +3,19 @@ TACC Tutorial 1. In home directory (`cdh`) make python 3.9 virtual environment: `python3 -m venv venv_39`. 2. Activate virtual environment: `source venv_39/bin/activate`. -3. In scratch directory (`cds`), download ilastik (`wget https://files.ilastik.org/ilastik-1.4.0-Linux.tar.bz2`). -4. Decompress the ilastik file (`tar –xvzf ilastik-1.4.0-Linux.tar.bz2`). -5. Clone brainlit repository (`git clone https://github.com/neurodata/brainlit.git`). -6. Install brainlit from source in editable mode: `cd brainlit && pip install -e .`. -7. Install packages I use for this tutorial: `pip install matplotlib-scalebar jupyter`. -8. Go back to the home directory (`cdh`) and copy the notebook I made: `cp /home1/09423/tathey1/brainline-tacc-tutorial.ipynb .`. -9. Create jupyter kernel for this virtual environment: `ipython kernel install --name "venv_39" --user`. -10. Open the jupyter notebook and select `venv_39` as the kernel. -11. As you run the notebook, you will need to change a couple variables including `brainlit_path` and `ilastik_path` according to your scratch directory path. +3. Update pip `pip install --upgrade pip` +4. In scratch directory (`cds`), download ilastik (`wget https://files.ilastik.org/ilastik-1.4.0-Linux.tar.bz2`). +5. Decompress the ilastik file (`tar –xvf ilastik-1.4.0-Linux.tar.bz2`). +6. Clone brainlit repository (`git clone https://github.com/neurodata/brainlit.git`). +7. Install brainlit from source in editable mode: `cd brainlit && pip install -e .`. +8. Install packages I use for this tutorial: `pip install matplotlib-scalebar jupyter`. +9. Go back to the home directory (`cdh`) and copy the notebook I made: `cp /home1/09423/tathey1/brainline-tacc-tutorial.ipynb .`. +10. Create jupyter kernel for this virtual environment: `ipython kernel install --name "venv_39" --user`. +11. Open the jupyter notebook and select `venv_39` as the kernel. +12. As you run the notebook, you will need to change a couple variables including `brainlit_path` and `ilastik_path` according to your scratch directory path. Atlas ----- -If you plan on using BrainLine analysis a lot (in particular, the napari coronal section views), I recommend you download the atlas from [here](https://neurodata.io/data/allen_atlas/). \ No newline at end of file +If you plan on using BrainLine analysis a lot (in particular, the napari coronal section views), I recommend you download the atlas from [here](https://neurodata.io/data/allen_atlas/). From 23c8a40be2aa094d431b6a91d79f5d6cbbb30e10 Mon Sep 17 00:00:00 2001 From: Thomas Athey Date: Tue, 23 May 2023 10:57:40 -0400 Subject: [PATCH 4/5] Update README.md --- docs/notebooks/pipelines/BrainLine/README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/notebooks/pipelines/BrainLine/README.md b/docs/notebooks/pipelines/BrainLine/README.md index 823e3160d..9c7463e61 100644 --- a/docs/notebooks/pipelines/BrainLine/README.md +++ b/docs/notebooks/pipelines/BrainLine/README.md @@ -1,6 +1,8 @@ TACC Tutorial ------------- +In Jupyter session on Lonestar 6: + 1. In home directory (`cdh`) make python 3.9 virtual environment: `python3 -m venv venv_39`. 2. Activate virtual environment: `source venv_39/bin/activate`. 3. Update pip `pip install --upgrade pip` From 5dd8c7dafd1d54457fa994e19b0b2c48c3701755 Mon Sep 17 00:00:00 2001 From: Thomas Athey Date: Tue, 23 May 2023 11:15:27 -0500 Subject: [PATCH 5/5] upgrade pip in netlify and circleci --- .circleci/config.yml | 1 + netlify.toml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 3bd95fc33..9d693d8ff 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -49,6 +49,7 @@ commands: command: | python3 -m venv venv . venv/bin/activate + pip install --upgrade pip pip install pytest pytest-cov black[jupyter] pip install -e . fork_test: diff --git a/netlify.toml b/netlify.toml index 984b15335..ae3571c02 100644 --- a/netlify.toml +++ b/netlify.toml @@ -11,7 +11,7 @@ publish = "docs/_build/html/" # Default build command. - command = "bash ./.aws.sh; pip install -U pip setuptools; pip install -r docs/requirements.txt; pip install -e .; cd docs; make html; cd .." + command = "bash ./.aws.sh; pip install --upgrade pip; pip install -U pip setuptools; pip install -r docs/requirements.txt; pip install -e .; cd docs; make html; cd .." # sudo apt-get update; sudo apt-get install python3.8 python3-pip; # Directory with the serverless Lambda functions to deploy to AWS.