Merge pull request #70 from Johannes-Sahlmann/ignore-case

Allow for flexible capitalization of instrument names

pysiaf/constants.py

@@ -7,24 +7,23 @@
 
 __all__ = ['JWST_PRD_VERSION', 'JWST_PRD_DATA_ROOT', 'HST_PRD_VERSION', 'HST_PRD_DATA_ROOT']
 
-_DATA_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'prd_data')
+_THIS_DIRECTORY = os.path.dirname(os.path.abspath(__file__))
 
-# _JWST_STAGING_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'staging_data')
-_JWST_TEMPORARY_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temporary_data')
+_DATA_ROOT = os.path.join(_THIS_DIRECTORY, 'prd_data')
 
-JWST_SOURCE_DATA_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'source_data')
+_JWST_TEMPORARY_ROOT = os.path.join(_THIS_DIRECTORY, 'temporary_data')
 
-JWST_TEMPORARY_DATA_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
-                                        'temporary_data')
+JWST_SOURCE_DATA_ROOT = os.path.join(_THIS_DIRECTORY, 'source_data')
 
-JWST_DELIVERY_DATA_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
-                                       'pre_delivery_data')
+JWST_TEMPORARY_DATA_ROOT = os.path.join(_THIS_DIRECTORY, 'temporary_data')
+
+JWST_DELIVERY_DATA_ROOT = os.path.join(_THIS_DIRECTORY, 'pre_delivery_data')
 
 # test data directory
-TEST_DATA_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'tests', 'test_data')
+TEST_DATA_ROOT = os.path.join(_THIS_DIRECTORY, 'tests', 'test_data')
 
 # directory for reports
-REPORTS_ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'reports')
+REPORTS_ROOT = os.path.join(_THIS_DIRECTORY, 'reports')
 
 AVAILABLE_PRD_JWST_VERSIONS = [os.path.basename(dir_name) for dir_name in
                                glob.glob(os.path.join(_DATA_ROOT, 'JWST', '*'))]

pysiaf/iando/read.py

@@ -21,7 +21,7 @@
 import lxml.etree as ET
 
 from ..constants import HST_PRD_DATA_ROOT, JWST_PRD_DATA_ROOT, JWST_SOURCE_DATA_ROOT
-
+from ..siaf import JWST_INSTRUMENT_NAME_MAPPING
 
 def get_siaf(input_siaf, observatory='JWST'):
     """Return a Siaf object corresponding to input_siaf which can be a string path or a Siaf object.
@@ -44,12 +44,12 @@ def get_siaf(input_siaf, observatory='JWST'):
         # initilize siaf as empty object
         siaf_object = siaf.Siaf(None)
         siaf_object.instrument = aperture_collection[list(aperture_collection.items())[0][0]].\
-            InstrName
+            InstrName.lower()
 
-        if siaf_object.instrument == 'NIRCAM':
-            siaf_object.instrument = 'NIRCam'
-        elif siaf_object.instrument == 'NIRSPEC':
-            siaf_object.instrument = 'NIRSpec'
+        # if siaf_object.instrument == 'NIRCAM':
+        #     siaf_object.instrument = 'NIRCam'
+        # elif siaf_object.instrument == 'NIRSPEC':
+        #     siaf_object.instrument = 'NIRSpec'
 
         siaf_object.apertures = aperture_collection
         siaf_object.description = os.path.basename(input_siaf)
@@ -256,9 +256,12 @@ def read_jwst_siaf(instrument=None, filename=None, basepath=None):
 
     Parameters
     ----------
-    instrument
-    filename
-    basepath
+    instrument : str
+        instrument name (case-insensitive)
+    filename : str
+        Absolute path to alternative SIAF xml file
+    basepath : str
+        Directory containing alternative SIAF xml file conforming with standard naming convention
 
     Returns
     -------
@@ -277,7 +280,8 @@ def read_jwst_siaf(instrument=None, filename=None, basepath=None):
         if not os.path.isdir(basepath):
             raise RuntimeError("Could not find SIAF data "
                                "in {}".format(basepath))
-        filename = os.path.join(basepath, instrument + '_SIAF.xml')
+        filename = os.path.join(basepath, JWST_INSTRUMENT_NAME_MAPPING[instrument.lower()]
+                                + '_SIAF.xml')
     else:
         filename = filename
 
@@ -377,18 +381,18 @@ def read_siaf_aperture_definitions(instrument):
 
     Parameters
     ----------
-    instrument
+    instrument : str
+        instrument name (case insensitive)
 
     Returns
     -------
     : astropy table
+        content of SIAF reference file
 
     """
-    filename = os.path.join(JWST_SOURCE_DATA_ROOT, instrument, '{}_siaf_aperture_definition.txt'.
-                            format(instrument.lower()))
+    filename = os.path.join(JWST_SOURCE_DATA_ROOT, JWST_INSTRUMENT_NAME_MAPPING[instrument.lower()],
+                            '{}_siaf_aperture_definition.txt'.format(instrument.lower()))
 
-    # converters = {'XDetRef': [ascii.convert_numpy(np.float32)]}
-    # , converters = converters, guess = False
     return Table.read(filename, format='ascii.basic', delimiter=',', fill_values=('None', 0))
 
 
@@ -397,14 +401,15 @@ def read_siaf_ddc_mapping_reference_file(instrument):
 
     Parameters
     ----------
-    instrument
+    instrument : str
+        instrument name (case insensitive)
 
     Returns
     -------
     : astropy table
 
     """
-    ddc_mapping_file = os.path.join(JWST_SOURCE_DATA_ROOT, instrument,
+    ddc_mapping_file = os.path.join(JWST_SOURCE_DATA_ROOT, JWST_INSTRUMENT_NAME_MAPPING[instrument.lower()],
                                     '{}_siaf_ddc_apername_mapping.txt'.format(instrument.lower()))
 
     ddc_mapping_table = Table.read(ddc_mapping_file, format='ascii.basic', delimiter=',')
@@ -435,15 +440,16 @@ def read_siaf_detector_reference_file(instrument):
 
     Parameters
     ----------
-    instrument
+    instrument : str
+        instrument name (case insensitive)
 
     Returns
     -------
     : astropy table
 
     """
-    filename = os.path.join(JWST_SOURCE_DATA_ROOT, instrument, '{}_siaf_detector_parameters.txt'.
-                            format(instrument.lower()))
+    filename = os.path.join(JWST_SOURCE_DATA_ROOT, JWST_INSTRUMENT_NAME_MAPPING[instrument.lower()],
+                            '{}_siaf_detector_parameters.txt'.format(instrument.lower()))
 
     return Table.read(filename, format='ascii.basic', delimiter=',')
 
@@ -453,15 +459,17 @@ def read_siaf_distortion_coefficients(instrument, aperture_name):
 
     Parameters
     ----------
-    instrument
-    aperture_name
+    instrument : str
+        instrument name (case insensitive)
+    aperture_name : str
+        name of master aperture
 
     Returns
     -------
     : astropy table
 
     """
-    distortion_reference_file_name = os.path.join(JWST_SOURCE_DATA_ROOT, instrument,
+    distortion_reference_file_name = os.path.join(JWST_SOURCE_DATA_ROOT, JWST_INSTRUMENT_NAME_MAPPING[instrument.lower()],
                                                   '{}_siaf_distortion_{}.txt'.format(
                                                       instrument.lower(), aperture_name.lower()))
 
@@ -473,13 +481,15 @@ def read_siaf_xml_field_format_reference_file(instrument):
 
     Parameters
     ----------
-    instrument
+    instrument  : str
+        instrument name (case insensitive)
 
     Returns
     -------
     : astropy table
 
     """
-    filename = os.path.join(JWST_SOURCE_DATA_ROOT, instrument, '{}_siaf_xml_field_format.txt'.
-                            format(instrument.lower()))
+    filename = os.path.join(JWST_SOURCE_DATA_ROOT, JWST_INSTRUMENT_NAME_MAPPING[instrument.lower()],
+                            '{}_siaf_xml_field_format.txt'.format(instrument.lower()))
+
     return Table.read(filename, format='ascii.basic', delimiter=',')

pysiaf/siaf.py

@@ -226,6 +226,15 @@ def plot_master_apertures(**kwargs):
         ax.set_xlim(xlim[::-1])
 
 
+ACCEPTED_INSTRUMENT_NAMES = 'nircam niriss miri nirspec fgs hst'.split()
+
+# mapping from internal lower-case names to mixed-case names used for xml file names
+JWST_INSTRUMENT_NAME_MAPPING = {'nircam': 'NIRCam',
+                                'nirspec': 'NIRSpec',
+                                'miri': 'MIRI',
+                                'niriss': 'NIRISS',
+                                'fgs': 'FGS'}
+
 class Siaf(ApertureCollection):
     """Science Instrument Aperture File class.
 
@@ -259,7 +268,7 @@ def __init__(self, instrument, filename=None, basepath=None, AperNames=None):
         Parameters
         -----------
         instrument : string
-            one of 'NIRCam', 'NIRSpec', 'NIRISS', 'MIRI', 'FGS'; case sensitive.
+            one of 'NIRCam', 'NIRSpec', 'NIRISS', 'MIRI', 'FGS'; case-insensitive.
         basepath : string
             Directory to look in for SIAF files
         filename : string, optional
@@ -268,20 +277,20 @@ def __init__(self, instrument, filename=None, basepath=None, AperNames=None):
         """
         super(Siaf, self).__init__()
 
-        if instrument is None:
-            return
+        if (instrument is None) or (isinstance(instrument, str) is False):
+            raise RuntimeError('Please specify a valid instrument name.')
 
-        elif instrument not in ['NIRCam', 'NIRSpec', 'NIRISS', 'MIRI', 'FGS', 'HST']:
-            raise ValueError('Invalid instrument name: {0}. Note that this is case '
-                             'sensitive.'.format(instrument))
+        elif instrument.lower() not in ACCEPTED_INSTRUMENT_NAMES:
+            raise ValueError('Invalid instrument name: {}. It has to be one of {} '
+                             '(case-insensitive).'.format(instrument, ACCEPTED_INSTRUMENT_NAMES))
 
-        self.instrument = instrument
+        self.instrument = instrument.lower()
 
-        if instrument == 'HST':
+        if self.instrument == 'hst':
             self.apertures = read.read_hst_siaf()
             self.observatory = 'HST'
         else:
-            self.apertures = read.read_jwst_siaf(instrument, filename=filename, basepath=basepath)
+            self.apertures = read.read_jwst_siaf(self.instrument, filename=filename, basepath=basepath)
             self.observatory = 'JWST'
 
     def __repr__(self):
@@ -295,19 +304,19 @@ def __str__(self):
     def _getFullApertures(self):
         """Return whichever subset of apertures correspond to the entire detectors."""
         fullaps = []
-        if self.instrument == 'NIRCam':
+        if self.instrument == 'nircam':
             fullaps.append(self.apertures['NRCA5_FULL'])
             fullaps.append(self.apertures['NRCB5_FULL'])
-        elif self.instrument == 'NIRSpec':
+        elif self.instrument == 'nirspec':
             fullaps.append(self.apertures['NRS_FULL_MSA1'])
             fullaps.append(self.apertures['NRS_FULL_MSA2'])
             fullaps.append(self.apertures['NRS_FULL_MSA3'])
             fullaps.append(self.apertures['NRS_FULL_MSA4'])
-        elif self.instrument == 'NIRISS':
+        elif self.instrument == 'niriss':
             fullaps.append(self.apertures['NIS_CEN'])
-        elif self.instrument == 'MIRI':
+        elif self.instrument == 'miri':
             fullaps.append(self.apertures['MIRIM_FULL'])
-        elif self.instrument == 'FGS':
+        elif self.instrument == 'fgs':
             fullaps.append(self.apertures['FGS1_FULL'])
             fullaps.append(self.apertures['FGS2_FULL'])
         return fullaps

pysiaf/tests/test_aperture.py

@@ -85,9 +85,9 @@ def test_jwst_aperture_transforms(siaf_objects, verbose=True, threshold=None):
 
     for siaf in siaf_objects:
         if threshold is None:
-            if siaf.instrument in ['MIRI']:
+            if siaf.instrument in ['miri']:
                 threshold = 0.2
-            elif siaf.instrument in ['NIRCam']:
+            elif siaf.instrument in ['nircam']:
                 threshold = 42.
             else:
                 threshold = 0.1
@@ -98,7 +98,7 @@ def test_jwst_aperture_transforms(siaf_objects, verbose=True, threshold=None):
             aperture = siaf[aper_name]
 
             if (aperture.AperType in ['COMPOUND', 'TRANSFORM']) or (
-                    siaf.instrument in ['NIRCam', 'MIRI', 'NIRSpec'] and
+                    siaf.instrument in ['nircam', 'miri', 'nirspec'] and
                     aperture.AperType == 'SLIT'):
                 skip = True
 
@@ -146,7 +146,7 @@ def test_jwst_aperture_vertices(siaf_objects):
             aperture = siaf[aper_name]
 
             if (aperture.AperType in ['COMPOUND', 'TRANSFORM']) or \
-                    (siaf.instrument in ['NIRCam', 'MIRI', 'NIRSpec']
+                    (siaf.instrument in ['nircam', 'miri', 'nirspec']
                      and aperture.AperType == 'SLIT'):
                 skip = True