fourth-order moments

docs/source/pipeline_canfar.md

@@ -121,27 +121,28 @@ patchnum=`tr $patch P ''`
 create_final_cat.py -m final_cat_$patch.hdf5 -i . -p $patch/cfis/final_cat.param -P $patchnum -o $patch/n_tiles_final.txt -v
 
 # Star catalogue
-combine_runs.bash  -p $psf -c psf
-shapepipe_run -c $SP_CONFIG/config_Ms_$psf.ini
-shapepipe_run -c $SP_CONFIG/config_Pl_$psf.ini
+
+## With fourth-order moment, combine additional psf interpol validation runs
+combine_runs.bash  -p $psf -c psf_val
 
 # Convert star cat to WCS
 ## Convert all input validation psf files and create directories par patch
 ## psf_conv_all/P?
-cd ../star_cat
+cd ../star_cat_val
 
-# Create files validation_psf_conv-<patchnum>-<idx>.fits
-# (for the v1.4 setup only one file)
- convert_psf_pix2world.py -i .. -P $patchnum -v
+## Create files validation_psf_conv-<patchnum>-<idx>.fits
+## (for the v1.4 setup only one file)
+## previous convert_psf_pix2world.py -i .. -P $patchnum -v
+for p in 1 2 3 4 5 6 7; do
+   convert_psf_pix2world.py -i .. -P $p --sub_dir_pattern=run_sp_combined_psf_val -v
+done
 
-# Combine previously created files as links within one SP run dir
-# (for the v1.4 setup only one link
-cd P$patch
+## Combine previously created files as links within one SP run dir
 combine_runs.bash -p psfex -c psf_conv
 
-# Merge all converted star catalogues and create final-starcat.fits
+## Merge all converted star catalogues and create final-starcat.fits
 export SP_RUN=`pwd`
-shapepipe_run -c ~/shapepipe/example/cfis/config_Ms_psfex_conv.ini
+shapepipe_run -c ~/shapepipe/example/cfis/config_Msval_psfex.ini
 
 
 # Extra stuff

example/cfis/config_Msval_psfex.ini

@@ -0,0 +1,71 @@
+# ShapePipe configuration file for post-processing.
+# merge star cat.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Msval
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = merge_starcat_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 4
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+[MERGE_STARCAT_RUNNER]
+
+INPUT_DIR = last:psfex_interp_runner
+
+PSF_MODEL = psfex
+
+#NUMBERING_SCHEME = -0000000-0
+NUMBERING_SCHEME = -0-0
+
+# Input file pattern(s), list of strings with length matching number of expected input file types
+# Cannot contain wild cards
+FILE_PATTERN = validation_psf_conv
+
+# FILE_EXT (optional) list of string extensions to identify input files
+FILE_EXT = .fits
+
+HDU = 1

example/cfis/config_exp_psfex_validation.ini

@@ -0,0 +1,82 @@
+# ShapePipe configuration file for single-exposures. PSFex PSF model
+# validation.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_Pv
+
+# Add date and time to RUN_NAME, optional, default: True
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = psfex_interp_runner
+
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[PSFEX_INTERP_RUNNER]
+
+# Use 20% sample for PSF validation
+FILE_PATTERN = star_split_ratio_80, star_split_ratio_20, psfex_cat
+
+FILE_EXT = .psf, .fits, .cat
+
+NUMBERING_SCHEME = -0000000-0
+
+# Run mode for psfex interpolation:
+#  CLASSIC: 'classical' run, interpolate to object positions
+#  MULTI-EPOCH: interpolate for multi-epoch images
+#  VALIDATION: validation for single-epoch images
+MODE = VALIDATION
+
+# Column names of position parameters
+POSITION_PARAMS = XWIN_IMAGE,YWIN_IMAGE
+
+# If True, measure and store ellipticity of the PSF (using moments)
+GET_SHAPES = True
+
+# Minimum number of stars per CCD for PSF model to be computed
+STAR_THRESH = 22
+
+# Maximum chi^2 for PSF model to be computed on CCD
+CHI2_THRESH = 2

pyproject.toml

@@ -9,7 +9,7 @@ authors = [
     { name = "Martin Kilbinger", email = "martin.kilbinger@cea.fr" }
 ]
 license = { "file" = "LICENSE" }
-requires-python = ">=3.11"
+requires-python = ">=3.9"
 dependencies = [
     "joblib>=0.13",
     "modopt>=1.2",
@@ -46,4 +46,22 @@ shapepipe_run = "shapepipe.shapepipe_run:main"
 
 [tool.pytest.ini_options]
 addopts = "--verbose --cov=shapepipe"
-testpaths = ["shapepipe"]
+testpaths = ["shapepipe"]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.data-files]
+"bin" = [
+    "scripts/sh/job_sp_canfar.bash",
+    "scripts/sh/init_run_exclusive_canfar.sh",
+    "scripts/sh/curl_canfar_local.sh",
+    "scripts/sh/functions.sh",
+    "scripts/sh/stats_jobs_canfar.sh",
+    "scripts/sh/combine_runs.bash",
+    "scripts/python/update_runs_log_file.py",
+    "scripts/python/summary_run.py",
+    "scripts/python/summary_params_pre_v2.py",
+    "scripts/python/link_to_exp_for_tile.py",
+    "scripts/python/convert_psf_pix2world.py",
+]