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Merge branch 'main' into operandi-372
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MehmedGIT committed Dec 3, 2024
2 parents f5611e8 + e31cd63 commit cfbef46
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Showing 18 changed files with 113 additions and 112 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ process ocrd_cis_ocropy_binarize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -110,7 +110,7 @@ process ocrd_anybaseocr_crop_1 {

script:
"""
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -134,7 +134,7 @@ process ocrd_skimage_binarize_2 {

script:
"""
${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
"""
}

Expand All @@ -158,7 +158,7 @@ process ocrd_skimage_denoise_3 {

script:
"""
${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
"""
}

Expand All @@ -182,7 +182,7 @@ process ocrd_tesserocr_deskew_4 {

script:
"""
${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
"""
}

Expand All @@ -206,7 +206,7 @@ process ocrd_cis_ocropy_segment_5 {

script:
"""
${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
"""
}

Expand All @@ -230,7 +230,7 @@ process ocrd_cis_ocropy_dewarp_6 {

script:
"""
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -254,7 +254,7 @@ process ocrd_calamari_recognize_7 {

script:
"""
${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
"""
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ process ocrd_cis_ocropy_binarize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -110,7 +110,7 @@ process ocrd_anybaseocr_crop_1 {

script:
"""
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -134,7 +134,7 @@ process ocrd_skimage_binarize_2 {

script:
"""
${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
"""
}

Expand All @@ -158,7 +158,7 @@ process ocrd_skimage_denoise_3 {

script:
"""
${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
"""
}

Expand All @@ -182,7 +182,7 @@ process ocrd_tesserocr_deskew_4 {

script:
"""
${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
"""
}

Expand All @@ -206,7 +206,7 @@ process ocrd_cis_ocropy_segment_5 {

script:
"""
${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
"""
}

Expand All @@ -230,7 +230,7 @@ process ocrd_cis_ocropy_dewarp_6 {

script:
"""
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -254,7 +254,7 @@ process ocrd_calamari_recognize_7 {

script:
"""
${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
"""
}

Expand Down
20 changes: 10 additions & 10 deletions src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ process ocrd_cis_ocropy_binarize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -114,7 +114,7 @@ process ocrd_anybaseocr_crop_1 {

script:
"""
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -138,7 +138,7 @@ process ocrd_cis_ocropy_denoise_2 {

script:
"""
${params.env_wrapper_cmd_step2} ocrd-cis-ocropy-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step2} ocrd-cis-ocropy-denoise -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -162,7 +162,7 @@ process ocrd_cis_ocropy_deskew_3 {

script:
"""
${params.env_wrapper_cmd_step3} ocrd-cis-ocropy-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
${params.env_wrapper_cmd_step3} ocrd-cis-ocropy-deskew -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
"""
}

Expand All @@ -186,7 +186,7 @@ process ocrd_tesserocr_segment_region_4 {

script:
"""
${params.env_wrapper_cmd_step4} ocrd-tesserocr-segment-region -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"padding": 5.0, "find_tables": false, "dpi": 300}'
${params.env_wrapper_cmd_step4} ocrd-tesserocr-segment-region -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"padding": 5.0, "find_tables": false, "dpi": 300}'
"""
}

Expand All @@ -210,7 +210,7 @@ process ocrd_segment_repair_5 {

script:
"""
${params.env_wrapper_cmd_step5} ocrd-segment-repair -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"plausibilize": true, "plausibilize_merge_min_overlap": 0.7}'
${params.env_wrapper_cmd_step5} ocrd-segment-repair -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"plausibilize": true, "plausibilize_merge_min_overlap": 0.7}'
"""
}

Expand All @@ -234,7 +234,7 @@ process ocrd_cis_ocropy_clip_6 {

script:
"""
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-clip -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-clip -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -258,7 +258,7 @@ process ocrd_cis_ocropy_segment_7 {

script:
"""
${params.env_wrapper_cmd_step7} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step7} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -282,7 +282,7 @@ process ocrd_cis_ocropy_dewarp_8 {

script:
"""
${params.env_wrapper_cmd_step8} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step8} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -306,7 +306,7 @@ process ocrd_tesserocr_recognize_9 {

script:
"""
${params.env_wrapper_cmd_step9} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"model": "Fraktur"}'
${params.env_wrapper_cmd_step9} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"model": "Fraktur"}'
"""
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ process ocrd_cis_ocropy_binarize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -114,7 +114,7 @@ process ocrd_anybaseocr_crop_1 {

script:
"""
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -138,7 +138,7 @@ process ocrd_cis_ocropy_denoise_2 {

script:
"""
${params.env_wrapper_cmd_step2} ocrd-cis-ocropy-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step2} ocrd-cis-ocropy-denoise -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -162,7 +162,7 @@ process ocrd_cis_ocropy_deskew_3 {

script:
"""
${params.env_wrapper_cmd_step3} ocrd-cis-ocropy-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
${params.env_wrapper_cmd_step3} ocrd-cis-ocropy-deskew -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
"""
}

Expand All @@ -186,7 +186,7 @@ process ocrd_tesserocr_segment_region_4 {

script:
"""
${params.env_wrapper_cmd_step4} ocrd-tesserocr-segment-region -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"padding": 5.0, "find_tables": false, "dpi": 300}'
${params.env_wrapper_cmd_step4} ocrd-tesserocr-segment-region -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"padding": 5.0, "find_tables": false, "dpi": 300}'
"""
}

Expand All @@ -210,7 +210,7 @@ process ocrd_segment_repair_5 {

script:
"""
${params.env_wrapper_cmd_step5} ocrd-segment-repair -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"plausibilize": true, "plausibilize_merge_min_overlap": 0.7}'
${params.env_wrapper_cmd_step5} ocrd-segment-repair -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"plausibilize": true, "plausibilize_merge_min_overlap": 0.7}'
"""
}

Expand All @@ -234,7 +234,7 @@ process ocrd_cis_ocropy_clip_6 {

script:
"""
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-clip -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-clip -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -258,7 +258,7 @@ process ocrd_cis_ocropy_segment_7 {

script:
"""
${params.env_wrapper_cmd_step7} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
${params.env_wrapper_cmd_step7} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
"""
}

Expand All @@ -282,7 +282,7 @@ process ocrd_cis_ocropy_dewarp_8 {

script:
"""
${params.env_wrapper_cmd_step8} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step8} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand All @@ -306,7 +306,7 @@ process ocrd_tesserocr_recognize_9 {

script:
"""
${params.env_wrapper_cmd_step9} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"model": "Fraktur"}'
${params.env_wrapper_cmd_step9} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"model": "Fraktur"}'
"""
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ process ocrd_tesserocr_recognize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"segmentation_level": "region", "textequiv_level": "word", "find_tables": true, "model": "deu"}'
${params.env_wrapper_cmd_step0} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"segmentation_level": "region", "textequiv_level": "word", "find_tables": true, "model": "deu"}'
"""
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ process ocrd_tesserocr_recognize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"segmentation_level": "region", "textequiv_level": "word", "find_tables": true, "model": "deu"}'
${params.env_wrapper_cmd_step0} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"segmentation_level": "region", "textequiv_level": "word", "find_tables": true, "model": "deu"}'
"""
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ process ocrd_cis_ocropy_binarize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ process ocrd_cis_ocropy_binarize_0 {

script:
"""
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} --page-id ${page_range} -I ${input_group} -O ${output_group}
"""
}

Expand Down
3 changes: 2 additions & 1 deletion src/utils/operandi_utils/oton/process_call_arguments.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
from logging import getLevelName, getLogger
from typing import Optional
from operandi_utils.oton.constants import (
BS, CONST_DIR_IN, CONST_DIR_OUT, CONST_WORKSPACE_DIR, CONST_METS_PATH, CONST_METS_SOCKET_PATH,
BS, CONST_DIR_IN, CONST_DIR_OUT, CONST_WORKSPACE_DIR, CONST_METS_PATH, CONST_PAGE_RANGE, CONST_METS_SOCKET_PATH,
OCRD_ALL_JSON, OTON_LOG_LEVEL
)

Expand Down Expand Up @@ -58,6 +58,7 @@ def dump_bash_form_with_placeholders(self):
dump += f' -U ${BS[0]}{CONST_METS_SOCKET_PATH}{BS[1]}'
dump += f' -w ${BS[0]}{CONST_WORKSPACE_DIR}{BS[1]}'
dump += f' -m ${BS[0]}{CONST_METS_PATH}{BS[1]}'
dump += f' --page-id ${BS[0]}{CONST_PAGE_RANGE}{BS[1]}'
dump += f' -I ${BS[0]}{CONST_DIR_IN}{BS[1]}'
dump += f' -O ${BS[0]}{CONST_DIR_OUT}{BS[1]}'
if self.parameters:
Expand Down
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