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HCS Parser: Create ome.tiff well by well #3251

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HCS Parser: Create ome.tiff well by well #3251

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0b082b5
HCS parser perform integrity check if asked, before perform actual work
SilinPavel May 23, 2023
3f1a8b1
HCS parser perform conversion well by well instead of whole sequence
SilinPavel May 25, 2023
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6 changes: 3 additions & 3 deletions deploy/docker/cp-tools/research/hcs-parser/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ RUN yum install -y curl \
openssh-server \
wget \
unzip \
python && \
python-devel && \
python \
python-devel \
gcc && \
curl https://cloud-pipeline-oss-builds.s3.amazonaws.com/tools/pip/2.7/get-pip.py | python - && \
pip install pillow==9.2.0 tifffile==2019.7.26.2 numpy==1.16.6 imagecodecs-lite==2019.12.3 pandas==0.24.2 openpyxl==2.6.4
Expand All @@ -51,7 +51,7 @@ RUN mkdir -p "$ANACONDA_HOME" && \
ImageMagick \
java-1.8.0-openjdk-devel && \
pip3 install $CP_PIP_EXTRA_ARGS -I -q generate-tiff-offsets==0.1.7 && \
pip3 install $CP_PIP_EXTRA_ARGS -I -q awscli
pip3 install $CP_PIP_EXTRA_ARGS -I -q awscli && \
conda deactivate

ARG BIOFORMATS_TO_RAW_VERSION=0.4.0
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7 changes: 4 additions & 3 deletions deploy/docker/cp-tools/research/hcs-parser/convert_to_ome_tiff.sh
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Expand Up @@ -17,13 +17,14 @@
INDEX_FILE_PATH="$1"
IMAGE_PREVIEW_DATA_ROOT="$2"
SEQUENCE_ID="$3"
OME_TIFF_IMAGE_NAME="$4"
WELL_ID="$4"
OME_TIFF_IMAGE_NAME="$5"

RAW_IMAGE_DIR=$(mktemp -d --dry-run "$IMAGE_PREVIEW_DATA_ROOT/$SEQUENCE_ID/data_XXXXX.raw/")
RAW_IMAGE_DIR=$(mktemp -d --dry-run "$IMAGE_PREVIEW_DATA_ROOT/$SEQUENCE_ID/$WELL_ID/data_XXXXX.raw/")
if [[ -z "$OME_TIFF_IMAGE_NAME" ]]; then
OME_TIFF_IMAGE_NAME="${HCS_PARSER_OME_TIFF_FILE_NAME:-data.ome.tiff}"
fi
OME_TIFF_IMAGE_PATH="$IMAGE_PREVIEW_DATA_ROOT/$SEQUENCE_ID/$OME_TIFF_IMAGE_NAME"
OME_TIFF_IMAGE_PATH="$IMAGE_PREVIEW_DATA_ROOT/$SEQUENCE_ID/$WELL_ID/$OME_TIFF_IMAGE_NAME"

HCS_PROCESSING_TASK="${HCS_PROCESSING_TASK:-HCS processing}"

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