debugged calib routine (1577b38e) · Commits · sns-hfir-scse / diffraction / nomad_calibration

cal_config.json

+4 −4

Original line number	Diff line number	Diff line
		{
		"Diamond": "/SNS/NOM/IPTS-35119/nexus/NOM_221552.nxs.h5",
		"Diamond": "/SNS/NOM/IPTS-36186/nexus/NOM_227151.nxs.h5",
		"Instrument": "NOM",
		"Date": "2025-08-20",
		"Date": "2025-09-08",
		"SampleEnv": "shifter",
		"OutputDir": "/SNS/NOM/shared/autoreduce/calibration",
		"GenShadowMask": "shadow_mask_shifter_221552.in",
		"GenShadowMask": "shadow_mask_shifter_227151.in",
		"DiaLattParam": 3.5671299351,
		"GroupMethod": "KMEANS_ED",
		"SaveInitCalTable": true,

nom_cal

+19 −14

Original line number	Diff line number	Diff line
		@@ -33,30 +33,30 @@ echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-

		# Generate mask
		if [ ! $gen_mask_file = "no" ]; then
		echo "[Info] Generating mask..."
		echo "[Info] Generating shadow mask..."
		mantidpython $working_dir/inputs/mask_gen/nom_shadow_mask_gen.py $dia_file
		rm -rf $running_dir/manual_mask_cache/gen_mask/$gen_mask_file
		Rscript $working_dir/inputs/mask_gen/find_dip.R $gen_mask_file
		cat $working_dir/inputs/mask.in \
		$running_dir/manual_mask_cache/gen_mask/$gen_mask_file \
		> $running_dir/mask_combined_cache.in
		echo "[Info] Done with mask shadow mask generation."
		else
		cat $working_dir/inputs/mask.in > $running_dir/mask_combined_cache.in
		fi

		cd $running_dir
		sed -i -r '/^\s*$/d' mask_combined_cache.in
		cp $running_dir/mask_combined_cache.in $running_dir/outputmask.txt

		if [ -d "tmp" ]; then
		rm -rf tmp
		fi

		cp autogrouping_config_template.json autogrouping_config.json
		sed -i "s%TO_REPLACE_CALIBRANT%${dia_file}%" autogrouping_config.json
		sed -i "s%TO_REPLACE_GM%${group_method}%" autogrouping_config.json
		sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json

		. /opt/anaconda/etc/profile.d/conda.sh
		# cp autogrouping_config_template.json autogrouping_config.json
		# sed -i "s%TO_REPLACE_CALIBRANT%${dia_file}%" autogrouping_config.json
		# sed -i "s%TO_REPLACE_GM%${group_method}%" autogrouping_config.json
		# sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json

		# # Grouping
		# # In case the `dev` environment is not working properly,
		@@ -78,17 +78,22 @@ sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json

		# External call to translate the mask file in plain text form to
		# its XML form.
		conda activate ~y8z/miniconda/envs/nom_calib
		echo "[Info] Extracting mask..."
		python group_calib_prep.py
		conda deactivate
		#. /opt/anaconda/etc/profile.d/conda.sh
		# conda activate ~y8z/miniconda/envs/nom_calib
		echo "[Info] Converting shadow mask file..."
		~y8z/miniconda/envs/nom_calib/bin/python group_calib_prep.py
		echo "[Info] Done with shadow mask converting."
		# conda deactivate

		cd $working_dir

		# Calibration
		echo "[Info] Calibrating..."
		# mantidpython $working_dir/utils/nom_cal.py $working_dir
		mantidpythonnightly $working_dir/utils/nom_cal.py $working_dir
		echo "[Info] calibrating..."
		mantidpython $working_dir/utils/nom_cal.py $working_dir
		# mantidpythonnightly $working_dir/utils/nom_cal.py $working_dir
		# ~y8z/miniconda/envs/mantid-developer-v6.13.1.2/bin/python /SNS/users/y8z/pd_utils/mantid_v6p13p1p2/build/bin/AddPythonPath.py
		# ~y8z/miniconda/envs/mantid-developer-v6.13.1.2/bin/python $working_dir/utils/nom_cal_local.py $working_dir $local_cc_file
		echo "[Info] Done with calibrating."

		if [ ! -d $out_dir/input_configs ] ; then
		mkdir $out_dir/input_configs

nom_cal_local

+15 −9

Original line number	Diff line number	Diff line
		@@ -41,23 +41,25 @@ if [ ! $gen_mask_file = "no" ]; then
		cat $working_dir/inputs/mask.in \
		$running_dir/manual_mask_cache/gen_mask/$gen_mask_file \
		> $running_dir/mask_combined_cache.in
		echo "[Info] Done with mask shadow mask generation."
		else
		cat $working_dir/inputs/mask.in > $running_dir/mask_combined_cache.in
		fi

		cd $running_dir
		sed -i -r '/^\s*$/d' mask_combined_cache.in
		cp $running_dir/mask_combined_cache.in $running_dir/outputmask.txt

		if [ -d "tmp" ]; then
		rm -rf tmp
		fi

		cp autogrouping_config_template.json autogrouping_config.json
		sed -i "s%TO_REPLACE_CALIBRANT%${dia_file}%" autogrouping_config.json
		sed -i "s%TO_REPLACE_GM%${group_method}%" autogrouping_config.json
		sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json
		# cp autogrouping_config_template.json autogrouping_config.json
		# sed -i "s%TO_REPLACE_CALIBRANT%${dia_file}%" autogrouping_config.json
		# sed -i "s%TO_REPLACE_GM%${group_method}%" autogrouping_config.json
		# sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json

		. /opt/anaconda/etc/profile.d/conda.sh
		# . /opt/anaconda/etc/profile.d/conda.sh

		# # Grouping
		# # In case the `dev` environment is not working properly,
		@@ -79,16 +81,20 @@ sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json

		# External call to translate the mask file in plain text form to
		# its XML form.
		conda activate ~y8z/miniconda/envs/nom_calib
		echo "[Info] Extracting mask..."
		python group_calib_prep.py
		conda deactivate
		# conda activate ~y8z/miniconda/envs/nom_calib
		echo "[Info] Converting shadow mask file..."
		~y8z/miniconda/envs/nom_calib/bin/python group_calib_prep.py
		echo "[Info] Done with shadow mask converting."
		# conda deactivate

		cd $working_dir

		# Calibration
		echo "[Info] Calibrating..."
		mantidpython $working_dir/utils/nom_cal_local.py $working_dir $local_cc_file
		# ~y8z/miniconda/envs/mantid-developer-v6.13.1.2/bin/python /SNS/users/y8z/pd_utils/mantid_v6p13p1p2/build/bin/AddPythonPath.py
		# ~y8z/miniconda/envs/mantid-developer-v6.13.1.2/bin/python $working_dir/utils/nom_cal_local.py $working_dir $local_cc_file
		echo "[Info] Done with calibrating."

		if [ ! -d $out_dir/input_configs ] ; then
		mkdir $out_dir/input_configs

utils/nom_cal.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -165,7 +165,7 @@ LoadDiffCal(InstrumentName="NOM",
		# calibration pipeline.
		LoadMask(Instrument="NOM",
		InputFile=os.path.join(working_dir,
		"inputs",
		".cache",
		input_config["MaskFile"]),
		OutputWorkspace="mask")
		MaskDetectors(Workspace="dia_calibrant",

utils/nom_cal_local.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -168,7 +168,7 @@ LoadDiffCal(InstrumentName="NOM",
		# calibration pipeline.
		LoadMask(Instrument="NOM",
		InputFile=os.path.join(working_dir,
		"inputs",
		".cache",
		input_config["MaskFile"]),
		OutputWorkspace="mask")
		MaskDetectors(Workspace="dia_calibrant",