Merge pull request #249 from simontorres/reference_lamps_name

Reference lamps name

docs/change_history.rst

@@ -5,6 +5,8 @@ Change History
 
 V1.2.0 Unreleased
 ^^^^^^^^^^^^^^^^^
+- Changed install instruction with exact steps and commands instead of
+  referencing documentation.
 - Improved method to detect saturated images. Added a table with the *half full
   well* for all the readout modes possible and created a method to easily
   retrieve the value. This is a big improvement since in earlier versions the

goodman_pipeline/core/core.py

@@ -798,9 +798,8 @@ def extract_fractional_pixel(ccd, target_trace, target_stddev, extraction_width,
                            comment="Aperture in first column")
 
             ccd.header.set('GSP_EXTR',
-                           value="{:.2f}:{:.2f} column {:d}".format(low_limit,
-                                                                    high_limit,
-                                                                    i+1))
+                           value="{:.2f}:{:.2f}".format(low_limit,
+                                                        high_limit))
 
             log.info("Extraction aperture in first column: {:s}".format(
                 ccd.header['GSP_EXTR']))
@@ -1947,7 +1946,14 @@ def save_extracted(ccd, destination, prefix='e', target_number=1):
         new_suffix = '_target_{:d}.fits'.format(target_number)
         file_name = re.sub('.fits', new_suffix, file_name)
 
-    new_file_name = prefix + file_name
+    if ccd.header['OBSTYPE'] == 'COMP':
+        extraction_region = re.sub(':','-', ccd.header['GSP_EXTR'])
+        file_name = re.sub('.fits', '_{:s}.fits'.format(extraction_region), file_name)
+        new_file_name = prefix + file_name
+
+    else:
+        new_file_name = prefix + file_name
+
     log.info("Saving uncalibrated(w) extracted spectrum to file: "
              "{:s}".format(new_file_name))
     full_path = os.path.join(destination, new_file_name)

goodman_pipeline/core/tests/test_core.py

@@ -850,15 +850,29 @@ def setUp(self):
         self.fake_image = CCDData(data=np.ones((100, 100)),
                                   meta=fits.Header(),
                                   unit='adu')
-        self.fake_image.header.set('CCDSUM',
-                                   value='1 1',
-                                   comment='Fake values')
 
         self.file_name = 'sample_file.fits'
         self.target_non_zero = 4
         self.current_directory = os.getcwd()
         self.full_path = os.path.join(self.current_directory, self.file_name)
         self.parent_file = 'parent_file.fits'
+
+        self.fake_image.header.set('CCDSUM',
+                                   value='1 1',
+                                   comment='Fake values')
+
+        self.fake_image.header.set('OBSTYPE',
+                                   value='OBJECT',
+                                   comment='Fake values')
+
+        self.fake_image.header.set('GSP_FNAM',
+                                   value=self.file_name,
+                                   comment='Fake values')
+
+        self.fake_image.header.set('GSP_PNAM',
+                                   value=self.parent_file,
+                                   comment='Fake values')
+
         self.fake_image.write(self.full_path, overwrite=False)
 
     def test_write_fits(self):
@@ -927,13 +941,20 @@ def test_save_extracted_target_non_zero(self):
                                            self.target_non_zero),
                                        self.file_name)))
 
+    def test_save_extracted_target_zero_comp(self):
+        self.fake_image.header.set('GSP_FNAM', value=self.file_name)
+        self.fake_image.header.set('OBSTYPE', value='COMP')
+        self.fake_image.header.set('GSP_EXTR', value='100.00:101.00')
+        same_fake_image = save_extracted(ccd=self.fake_image,
+                                         destination=self.current_directory,
+                                         prefix='e',
+                                         target_number=0)
+
+        self.assertEqual(same_fake_image, self.fake_image)
+        self.assertTrue(os.path.isfile(self.fake_image.header['GSP_FNAM']))
+
     def tearDown(self):
-        files_to_remove = [self.full_path,
-                           'e' + self.file_name,
-                           'e' + re.sub('.fits',
-                                        '_target_{:d}.fits'.format(
-                                            self.target_non_zero),
-                                        self.file_name)]
+        files_to_remove = [self.full_path, self.fake_image.header['GSP_FNAM']]
 
         for _file in files_to_remove:
             if os.path.isfile(_file):

goodman_pipeline/spectroscopy/redspec.py

@@ -398,18 +398,21 @@ def _run(self, data_container, extraction_type):
                                 target_trace=single_trace,
                                 spatial_profile=single_profile,
                                 extraction_name=extraction_type)
-                            saved_ccd = save_extracted(ccd=extracted,
-                                                      destination=self.args.destination,
-                                                      target_number=target_number)
+                            saved_ccd = save_extracted(
+                                ccd=extracted,
+                                destination=self.args.destination,
+                                target_number=target_number)
                             # print(spec_file)
 
                             # lamp extraction
                             all_lamps = []
                             if comp_ccd_list:
                                 for comp_lamp in comp_ccd_list:
-                                    comp_lamp.header.set('GSP_SCTR',
-                                                         value=saved_ccd.header['GSP_FNAM'],
-                                                         comment='Science target file the lamp was extracted for.')
+                                    comp_lamp.header.set(
+                                        'GSP_SCTR',
+                                        value=saved_ccd.header['GSP_FNAM'],
+                                        comment='Science target file the lamp '
+                                                'was extracted for.')
 
                                     comp_lamp = record_trace_information(ccd=comp_lamp,
                                                                          trace_info=trace_info)
@@ -446,7 +449,6 @@ def _run(self, data_container, extraction_type):
                                 elif plt.get_backend() == u'Qt5Agg':
                                     manager.window.showMaximized()
 
-
                                 ax.set_title(
                                     "{:s} Extraction centered near "
                                     "{:.2f} \n File: {:s}".format(

goodman_pipeline/spectroscopy/wavelength.py

@@ -225,7 +225,7 @@ def __call__(self,
                         lamp=True)
 
                     wavelength_solutions.append(self.wsolution)
-                    reference_lamp_names.append(self.calibration_lamp)
+                    reference_lamp_names.append(self.wcal_lamp_file)
                 else:
                     self.log.error('It was not possible to get a wavelength '
                                    'solution from lamp '
@@ -242,12 +242,12 @@ def __call__(self,
                 for i in range(len(wavelength_solutions)):
                     # TODO (simon): Combine Multiple solutions
                     self.wsolution = wavelength_solutions[i]
-                    self.calibration_lamp = reference_lamp_names[i]
+                    self.wcal_lamp_file = reference_lamp_names[i]
                     self._save_science_data(ccd=ccd, index=i + 1)
 
             elif len(wavelength_solutions) == 1:
                 self.wsolution = wavelength_solutions[0]
-                self.calibration_lamp = reference_lamp_names[0]
+                self.wcal_lamp_file = reference_lamp_names[0]
                 self._save_science_data(ccd=ccd)
             else:
                 self.log.error("No wavelength solution.")
@@ -1293,7 +1293,7 @@ def _save_wavelength_calibrated(self,
         if index is None:
             f_end = '.fits'
         else:
-            f_end = '_{:d}.fits'.format(index)
+            f_end = '_ws_{:d}.fits'.format(index)
 
         new_filename = os.path.join(self.args.destination,
                                     self.args.output_prefix +