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Fixed installation issues of #3 #4

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Fixed installation issues of #3 #4

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d914662
Code Review and dependencies update
spirosmaggioros Aug 13, 2024
441a543
remove unused lines of code
spirosmaggioros Aug 13, 2024
8ffa779
realpath bug fix
spirosmaggioros Aug 13, 2024
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7 changes: 3 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# **NiChart<sup>Workflows</sup>**
# **NiChart<sup>Workflows</sup>**

A toolkit that allows users to apply **NiChart** processing methods and pre-trained models on their data. **NiChart<sup>Workflows</sup>** includes tools for [data harmonization](https://neuroimagingchart.com/components/#Harmonization) and [machine learning](https://neuroimagingchart.com/components/#Machine%20Learning), using pre-trained models and reference distributions provided by [**NiChart<sup>Engine</sup>**](https://github.com/gurayerus/NiChart_Engine). **NiChart<sup>Workflow</sup>** utilizes [Snakemake](https://snakemake.github.io) workflows to define multi-step image processing and data analytics pipelines.

Expand All @@ -13,7 +13,7 @@ Install dependencies for the **NiChart<sup>Workflows</sup>** in a conda environm
```bash
conda install -n base -c conda-forge mamba # If needed
mamba init # If first time installing, then potentially source ~/.bashrc
mamba create -c conda-forge -c bioconda -n NiChart_Workflows python=3.8
mamba create -c conda-forge -c bioconda -n NiChart_Workflows python=3.12
mamba activate NiChart_Workflows
pip install NiChart-Viewer-Demo spare-scores NiChartHarmonize
mamba install -c conda-forge -c bioconda snakemake
Expand Down Expand Up @@ -58,7 +58,7 @@ If the workflow works successfully, workflow steps will be run on the data. Resu

> "../../output/vTest1",

and the viewer will be launched with the combined result file as input.
and the viewer will be launched with the combined result file as input.

## Contributing:

Expand All @@ -76,4 +76,3 @@ This project is licensed under the [License Name] license. Please refer to the L
## Contact:

For any inquiries, please contact [email protected]. (Last Updated: 5/24/2024)

1 change: 1 addition & 0 deletions input/vTest2/Study1/Images/Images
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Hi @spirosmaggioros , is this a symlink for your testing? Maybe add this filepath pattern to .gitignore.

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yeah sure, i though it was already in the gitignore but it didnt, git status didnt show me this.
Also, as you see i clone the DLMUSE directly and build it from the repo. I downloaded the nnUNet model folder from the tag and manually put it inside the w_sMRI folder(where the snakefile is located). So this is pretty much my work-folder. I will make it more user friendly in the future, i just have to find a way to fully run it first :)

Original file line number Diff line number Diff line change
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/Users/spirosmag/Documents/NiChart_Workflows/input/vTest2/Study1/Images
21 changes: 17 additions & 4 deletions utils/dlmuse/util_dlmuse_apply.sh
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@@ -1,10 +1,23 @@
#! /bin/bash -x

# download NiChart DLMUSE package
echo "Downloading NiChart DLMUSE..."
if [ -d "/NiChart_DLMUSE" ]
then
echo "Clone already exists!"
else
git clone https://github.com/CBICA/NiChart_DLMUSE.git
fi
cd NiChart_DLMUSE
pip install .
cd ..
echo "NiChart DLMUSE downloaded!"
echo "About to run: $0 $@"


## Read input
in_csv=$(realpath $1)
out_csv=$(realpath $2)
out_csv=$2

## Prep init data
in_dir=$(dirname ${in_csv})
Expand All @@ -14,10 +27,10 @@ tmp_dir="${out_dir}/tmprun_dlmuse"
mkdir -pv "${tmp_dir}/nnUNet_preprocessed"
mkdir -pv "${tmp_dir}/nnUNet_raw_database"
mkdir -pv "${tmp_dir}/nnUNet_out"
ln -s `realpath ../../../../NiChart/NiChart_Models/nnUNet_model` ${tmp_dir}/nnUNet_model
ln -s `realpath ./nnUNet_model` "${tmp_dir}/nnUNet_model"
ln -s `realpath ${in_dir}/Images` "${tmp_dir}/nnUNet_raw_database/nnUNet_raw_data"
droi=`realpath ../../../../NiChart/NiChart_DLMUSE/shared/dicts/MUSE_mapping_derived_rois.csv`
roi=`realpath ../../../../NiChart/NiChart_DLMUSE/shared/dicts/MUSE_mapping_consecutive_indices.csv`
droi=`realpath NiChart_DLMUSE/shared/dicts/MUSE_mapping_derived_rois.csv`
roi=`realpath NiChart_DLMUSE/shared/dicts/MUSE_mapping_consecutive_indices.csv`

## Apply dlmuse test
cmd="NiChart_DLMUSE --indir ${tmp_dir}/nnUNet_raw_database/nnUNet_raw_data --outdir ${tmp_dir}/nnUNet_out --pipelinetype structural --derived_ROI_mappings_file $droi --MUSE_ROI_mappings_file $roi --nnUNet_raw_data_base ${tmp_dir}/nnUNet_raw_database --nnUNet_preprocessed ${tmp_dir}/nnUNet_preprocessed --model_folder ${tmp_dir}/nnUNet_model --all_in_gpu True --mode fastest --disable_tta"
Expand Down
15 changes: 15 additions & 0 deletions utils/spare/util_spare_test.sh
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@@ -1,5 +1,20 @@
#! /bin/bash

# download spare package
echo "Downloading spare score package..."
if [ -d "/spare_score" ]
then
echo "spare score clone already exists!"
else
git clone https://github.com/CBICA/spare_score.git
fi
python setup.py bdist_wheel
cd dist
WHEEL_FILE=$(ls spare_scores*)
pip install "$WHEEL_FILE"
cd ..
echo "spare score is downloaded!"

## Read input
in_csv=$1
in_mdl=$2
Expand Down
8 changes: 4 additions & 4 deletions workflows/w_sMRI/Snakefile
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Expand Up @@ -9,10 +9,10 @@ import os
#report: "report/workflow.rst"

###################################
## Default config file
## Default config file
## Runs the workflow with the test dataset
## Edit this for running it on other datasets
in_config = "../../config/vTest1/config.yaml"
in_config = "../../config/vTest2/config.yaml"
#in_config = "../../config/vTest2/config.yaml"
configfile: f"{in_config}"
###################################
Expand Down Expand Up @@ -192,7 +192,7 @@ rule calc_derived_ROIs:
'''
Calculate derived ROIs from harmonized data
- If the input data already includes derived ROIs, they will not be updated
'''
'''
input:
in_csv=f"../../{dir_output}/{{study}}/out_combat/{{study}}_{{dtype}}_COMBAT_single.csv",
dict=f"../../{derived_rois}"
Expand Down Expand Up @@ -293,7 +293,7 @@ rule launch_viewer:
touch(f"../../{dir_output}/flag_VIEWED.csv"),
shell:
"NiChart_Viewer --data_file {input}"

## Delete flag for the viewer, so that it will launch the viewer next time
if os.path.exists(f"../../{dir_output}/flag_VIEWED.csv"):
os.remove(f"../../{dir_output}/flag_VIEWED.csv")