split exposure runner standardisation

shapepipe/modules/split_exp_package/split_exp_script.py

@@ -0,0 +1,139 @@
+# -*- coding: utf-8 -*-
+"""SPLIT EXP SCRIPT
+
+Class to split single-exposure multi-CCD mosaic images into single-exposure single-CCD
+files, one HDU per CCD.
+
+:Author: Axel Guinot
+
+:Date: 2019, 2020
+
+:Package: ShapePipe
+
+"""
+
+import numpy as np
+import sip_tpv as stp
+from astropy.wcs import WCS
+from astropy.io import fits
+
+from shapepipe.pipeline import file_io as io
+
+
+class SplitExposures(object):
+    """Split Exposures initialisation
+
+    Parameters
+    ----------
+    input_file_list : list of strings
+        input file paths, typically image, weight, and flag
+    output_dir : string
+        output directory
+    file_number_string : string
+        input file identified
+    output_suffix : string
+        output file suffix
+    n_hdu : int
+        number of HDUs (= CCDs) of input files
+    """
+
+    def __init__(
+        self,
+        input_file_list,
+        output_dir,
+        file_number_string,
+        output_suffix,
+        n_hdu
+    ):
+
+        self._input_file_list = input_file_list
+        self._output_dir = output_dir
+        self._file_number_string = file_number_string
+        self._output_suffix = output_suffix
+        self._n_hdu = n_hdu
+
+    def process(self):
+        """Process
+
+        Process the splitting of single-exposure images
+        """
+
+        for exp_path, output_suffix in zip(
+            self._input_file_list,
+            self._output_suffix
+        ):
+
+            transf_int = 'flag' in output_suffix
+            transf_coord = 'image' in output_suffix
+            save_header = 'image' in output_suffix
+
+            self.create_hdus(
+                exp_path,
+                output_suffix,
+                transf_coord,
+                transf_int,
+                save_header
+            )
+
+    def create_hdus(
+        self,
+        exp_path,
+        output_suffix,
+        transf_coord,
+        transf_int,
+        save_header
+    ):
+        """ Create HDUs
+
+        Split a single exposures CCDs into separate files.
+
+        Parameters
+        ----------
+        exp_path : str
+            Path to the single exposure
+        output_suffix : str
+            Suffix for the output file
+        transf_coord : bool
+            Transform the WCS (pv to sip) if True
+        transf_int : bool
+            Set data types to int if True
+        save_header : bool
+            Save WCS information if True
+        """
+
+        header_file = np.zeros(self._n_hdu, dtype='O')
+
+        for i in range(1, self._n_hdu+1):
+
+            h = fits.getheader(exp_path, i)
+            if transf_coord:
+                stp.pv_to_sip(h)
+
+            d = fits.getdata(exp_path, i)
+            if transf_int:
+                d = d.astype(np.int16)
+
+            file_name = (
+                f'{self._output_dir}/{output_suffix}'
+                + '{self._file_number_string}-{str(i-1)}.fits'
+            )
+
+            new_file = io.FITSCatalog(
+                file_name,
+                open_mode=io.BaseCatalog.OpenMode.ReadWrite
+            )
+            new_file.save_as_fits(data=d, image=True, image_header=h)
+
+            if save_header:
+                try:
+                    w = WCS(h)
+                except:
+                    print(f'WCS error for file {exp_path}')
+                    raise
+                header_file[i-1] = {'WCS': w, 'header': h.tostring()}
+
+        if save_header:
+            file_name = (
+                f'{self._output_dir}/headers{self._file_number_string}.npy'
+            )
+            np.save(file_name, header_file)

shapepipe/modules/split_exp_runner.py

@@ -2,93 +2,49 @@
 
 """SPLIT EXP RUNNER
 
-This module split the different CCD's hdu of a single exposure into separate
-files.
+This module splits the different CCDs (= hdus in FITS files) of a
+single exposure into separate files.
 
 :Author: Axel Guinot
 
-"""
-
-
-import numpy as np
-import sip_tpv as stp
-from astropy.wcs import WCS
-from astropy.io import fits
-
-from shapepipe.modules.module_decorator import module_runner
-from shapepipe.pipeline import file_io as io
-
-
-def create_hdus(exp_path, output_dir, output_name, output_sufix, n_hdu=40,
-                transf_coord=True, transf_int=False, save_header=False):
-    """ Create HDUs
-
-    Split a single exposures CCDs into separate files.
-
-    exp_path : str
-        Path to the single exp.
-    output_dir : str
-        Path to the output directory.
-    output_sufix : str
-        Suffix for the output file.
-    n_hdu : int
-        Number of HDUs (i.e. : number of CCDs).
-    transf_coord : bool
-        If True will transform the WCS (pv to sip).
-    transf_int : bool
-        If True will set datas to int.
-    save_header : bool
-        If True will save WCS information
-
-    """
+:Date: 2019, 2020
 
-    header_file = np.zeros(n_hdu, dtype='O')
-
-    for i in range(1, n_hdu+1):
-
-        h = fits.getheader(exp_path, i)
-        if transf_coord:
-            stp.pv_to_sip(h)
-
-        d = fits.getdata(exp_path, i)
-        if transf_int:
-            d = d.astype(np.int16)
-
-        file_name = (output_dir + '/' + output_sufix + output_name +
-                     '-' + str(i-1) + '.fits')
-        new_file = io.FITSCatalog(file_name,
-                                  open_mode=io.BaseCatalog.OpenMode.ReadWrite)
-        new_file.save_as_fits(data=d, image=True, image_header=h)
-
-        if save_header:
-            try:
-                w = WCS(h)
-            except:
-                print('WCS error for file {}'.format(exp_path))
-                raise
-            header_file[i-1] = {'WCS': w, 'header': h.tostring()}
-
-    if save_header:
-        file_name = output_dir + '/' + 'headers' + output_name + '.npy'
-        np.save(file_name, header_file)
+:Package: ShapePipe
 
+"""
 
-@module_runner(version='1.0', file_pattern=['image', 'weight', 'flag'],
-               file_ext=['.fz', '.fz', '.fz'],
-               depends=['numpy', 'astropy', 'sip_tpv'])
-def split_exp_runner(input_file_list, run_dirs, file_number_string,
-                     config, w_log):
 
-    file_suffix = config.getlist("SPLIT_EXP_RUNNER", "OUTPUT_SUFFIX")
+from shapepipe.modules.module_decorator import module_runner
+from shapepipe.modules.split_exp_package import split_exp_script as split
+
+
+@module_runner(
+    version='1.0',
+    input_module='get_images_runner',
+    file_pattern=['image', 'weight', 'flag'],
+    file_ext=['.fz', '.fz', '.fz'],
+    depends=['numpy', 'astropy', 'sip_tpv'],
+    run_method='parallel'
+)
+def split_exp_runner(
+    input_file_list,
+    run_dirs,
+    file_number_string,
+    config,
+    w_log
+):
+
+    output_suffix = config.getlist("SPLIT_EXP_RUNNER", "OUTPUT_SUFFIX")
     n_hdu = config.getint("SPLIT_EXP_RUNNER", "N_HDU")
 
-    for exp_path, exp_suffix in zip(input_file_list, file_suffix):
-
-        transf_int = 'flag' in exp_suffix
-        transf_coord = 'image' in exp_suffix
-        save_header = 'image' in exp_suffix
+    inst = split.SplitExposures(
+        input_file_list,
+        run_dirs['output'],
+        file_number_string,
+        output_suffix,
+        n_hdu
+    )
 
-        create_hdus(exp_path, run_dirs['output'], file_number_string,
-                    exp_suffix, n_hdu, transf_coord, transf_int, save_header)
+    inst.process()
 
     return None, None