Commit af9e3ed0 authored by Zhang, Yuanpeng's avatar Zhang, Yuanpeng ⭐
Browse files

fix the issue with shadow mask generation config

parent c4561c24

README.md

+9 −9
Original line number Diff line number Diff line
@@ -21,7 +21,7 @@ Here is a typical input configuration file (in JSON format), 
    "SampleEnv": "Shifter",

    "OutputDir": "/SNS/NOM/shared/CALIBRATION/2023_1_1A_Group_CAL",

    "DiaLattParam": 3.5671299351,

    "GenShadowMask": true,

    "GenShadowMask": "shadow_mask.in",

    "GroupMethod": "KMEANS_ED",

    "SaveInitCalTable": true,

    "Quiet": true,
@@ -36,14 +36,14 @@ detailed information, 


> DOI: 10.1103/PhysRevLett.104.085901



The `GenShadowMask` entry is for controlling whether to generate the masks for

the shadowed region of the detectors. The `GroupMethod` entry specifies the

method to be used for grouping pixels initially before the calibration.

Currently, the grouping of pixels is only used for identifying those pixels

which are far away from others and thus will be treated as outliers and masked

out. The `SaveInitCalTable` flag is for specifying whether to save the

intermediate calibration where all pixels are lined up without further

calibration. The `Quiet` flag controls whether to print out logs during the

The `GenShadowMask` entry is for specifying the file name of the generated masks for

the shadowed region of the detectors. If the entry is not given, no shadow mask will

be generated.  The `GroupMethod` entry specifies the method to be used for grouping

pixels initially before the calibration. Currently, the grouping of pixels is only

used for identifying those pixels which are far away from others and thus will be

treated as outliers and masked out. The `SaveInitCalTable` flag is for specifying

whether to save the intermediate calibration where all pixels are lined up without

further calibration. The `Quiet` flag controls whether to print out logs during the

running. By suppressing the console log output, one can save a lot of wall time.

The `ArbCalFile` entry specifies an arbitrary starting calibration file. This is

to be used as the input calibration file for running the `PDCalibration`

cal_config.json

+1 −1
Original line number Diff line number Diff line
@@ -5,7 +5,7 @@ 
    "SampleEnv": "Shifter",

    "OutputDir": "/SNS/NOM/shared/CALIBRATION/2023_1_1A_Group_CAL",

    "DiaLattParam": 3.5671299351,

    "GenShadowMask": true,

    "GenShadowMask": "shadow_mask.in",

    "GroupMethod": "KMEANS_ED",

    "SaveInitCalTable": true,

    "Quiet": true,

nom_cal

+1 −1
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ echo "Output directory: $out_dir" 
echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+"



# Generate mask

if [ $gen_mask_file = "yes" ]; then

if [ ! $gen_mask_file = "no" ]; then

    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

nom_cal_dev

+1 −1
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ echo "Output directory: $out_dir" 
echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+"



# Generate mask

if [ $gen_mask_file = "yes" ]; then

if [ ! $gen_mask_file = "no" ]; then

    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

utils/mg_config.py

+3 −4
Original line number Diff line number Diff line
@@ -5,9 +5,8 @@ input_config_f = sys.argv[1] 
with open(input_config_f, "r") as f:

    input_config = json.load(f)



if "GenShadowMask" in input_config:

    gen_mask = input_config["GenShadowMask"]



if gen_mask:

    print("yes")

    print(gen_mask)

else:

    print("no")