Mostly GUI Bugfixes

eispac/core/read_cube.py

@@ -14,7 +14,7 @@
 from eispac.core.read_wininfo import read_wininfo
 from eispac.instr.calc_read_noise import calc_read_noise
 
-def read_cube(filename=None, window=0, apply_radcal=True, radcal=None,
+def read_cube(filename=None, window=0, exp_set='sum', apply_radcal=True, radcal=None,
               abs_errs=True, count_offset=None, debug=False):
     """Load a single window of EIS data from an HDF5 file into an EISCube object
 
@@ -25,6 +25,11 @@ def read_cube(filename=None, window=0, apply_radcal=True, radcal=None,
     window : int, float, or str, optional
         Requested spectral window number or the value of any wavelength within
         the requested window. Default is '0'
+    exp_set : int or str, optional
+        Index number of the exposure set to load from the file. Only used in the 
+        rare case of scanning observations with multiple exposures per raster 
+        position. Can also set to a value of "sum" to add together all exposures 
+        and simulate a longer exposure image. Default is "sum".
     apply_radcal : bool, optional
         If set to True, will apply the pre-flight radiometric calibration curve
         found in the HDF5 header file and set units to erg/(cm^2 s sr). If set
@@ -179,13 +184,15 @@ def read_cube(filename=None, window=0, apply_radcal=True, radcal=None,
             meta['date_obs'] = np.array(f_head['times/date_obs']).astype(np.str_)
             meta['date_obs_format'] = np.array(f_head['times/time_format']).astype(np.str_)[0]
         except KeyError:
+            # Estimate missing or broken timestamps (ideally, never used)
             print('WARNING: the header file has missing or incomplete date_obs' 
                  +' for each raster step! Filling with estimated timestamps.')
             total_time = np.datetime64(index['date_end']) - np.datetime64(index['date_obs'])
             total_time = total_time / np.timedelta64(1, 's') # ensure [s] units
-            est_cad = total_time / index['nexp']
+            n_xsteps = index['nexp'] / index['nexp_prp']
+            est_cad = total_time / n_xsteps
             est_date_obs = np.datetime64(index['date_obs']) \
-                         + np.arange(index['nexp']) \
+                         + np.arange(n_xsteps) \
                          * np.timedelta64(int(est_cad*1000), 'ms')
             if index['nraster'] == 1:
                 # Sit-and-stare timestamps inc left to right
@@ -221,6 +228,73 @@ def read_cube(filename=None, window=0, apply_radcal=True, radcal=None,
     else:
         radcal_array = None
 
+    ############################################################################
+    ### Check for multiple exposure sets and select one (very rarely used)
+    ############################################################################
+    if len(lv_1_counts.shape) == 4:
+        nexp_per_pos = lv_1_counts.shape[0] # Num exposures per slit position
+
+        if not isinstance(exp_set, (str, int)):
+            print(f"ERROR: invalid 'raster' keyword data type. Please input a"
+                 +f" string of 'sum' or an integer.", file=sys.stderr)
+            return None
+        elif isinstance(exp_set, str):
+            if exp_set.isdigit():
+                # convert string containing an integer
+                exp_set = int(exp_set)
+            elif exp_set.lower() != 'sum':
+                print(f"ERROR: invalid raster string of '{exp_set}'. Please"
+                     +f" input either 'sum' or an integer between 0 and"
+                     +f" {nexp_per_pos-1}.", file=sys.stderr)
+                return None
+
+        if isinstance(exp_set, int):
+            if (exp_set >= nexp_per_pos) or (exp_set < -1*nexp_per_pos):
+                # Check for out-of-bound indices
+                oob_exp_set = exp_set
+                if exp_set < 0:
+                    exp_set = 0
+                else:
+                    exp_set = nexp_per_pos-1
+                print(f"WARNING: exp_set {oob_exp_set} is out of bounds."
+                     +f" Loading the nearest valid exp_set ({exp_set}) instead.", 
+                     file=sys.stderr)
+            elif exp_set < 0:
+                # convert negative indices to positive
+                exp_set = nexp_per_pos - exp_set
+
+        # Extract the correct subarrays
+        if str(exp_set).lower() == 'sum':
+            print(f'Summing all {nexp_per_pos} sets exposures per slit position')
+            lv_1_counts = np.nansum(lv_1_counts, axis=0)
+            meta['date_obs'] = meta['date_obs'][0, :]
+            meta['duration'] = np.nansum(meta['duration'], axis=0)
+            meta['wave_corr'] = np.nanmean(meta['wave_corr'], axis=0)
+            meta['wave_corr_t'] = np.nanmean(meta['wave_corr_t'], axis=0)
+            meta['pointing']['solar_x'] = meta['pointing']['solar_x'][0, :]
+        else:
+            print(f'Loading exposure set {exp_set} ({exp_set+1} of {nexp_per_pos})')
+            lv_1_counts = lv_1_counts[exp_set,:,:,:]
+            meta['date_obs'] = meta['date_obs'][exp_set, :]
+            meta['duration'] = meta['duration'][exp_set, :]
+            meta['wave_corr'] = meta['wave_corr'][exp_set, :, :]
+            meta['wave_corr_t'] = meta['wave_corr_t'][exp_set, :]
+            meta['pointing']['solar_x'] = meta['pointing']['solar_x'][exp_set, :]
+    elif len(lv_1_counts.shape) > 4:
+        print(f"ERROR: cannot read input file with data array shape of"
+             +f" {lv_1_counts.shape}.", file=sys.stderr)
+        return None
+
+    ############################################################################
+    ### Determine observation type
+    ############################################################################
+    if index['nraster'] == 1:
+        obs_type = 'sit-and-stare'
+    elif index['nexp_prp'] >= 2:
+        obs_type = 'multi_scan'
+    else:
+        obs_type = 'scan'
+
     ############################################################################
     ### Apply pointing corrections and create output EISCube
     ############################################################################
@@ -240,10 +314,6 @@ def read_cube(filename=None, window=0, apply_radcal=True, radcal=None,
 
     ### (3) Apply wave correction and get median base wavelength value and delta
     counts_shape = lv_1_counts.shape
-    if len(counts_shape) > 3:
-        print('ERROR: EIS observations with multiple rasters in a single file'
-             +' are not currently supported.', file=sys.stderr)
-        return None
     ny_pxls = counts_shape[0] # num pixels along the slit (y-axis)
     nx_steps = counts_shape[1] # num raster steps (x-axis)
     n_wave = counts_shape[2] # num wavelength values (i.e. EIS window width)
@@ -297,7 +367,10 @@ def read_cube(filename=None, window=0, apply_radcal=True, radcal=None,
     output_hdr['bunit'] = 'unknown' # units of primary observable
     output_hdr['slit_id'] = index['slit_id']
     output_hdr['slit_ind'] = index['slit_ind']
+    output_hdr['obs_type'] = obs_type
     output_hdr['nraster'] = index['nraster'] # 1 for sit-and-stare
+    output_hdr['nexp'] = index['nexp'] # total num exposures
+    output_hdr['nexp_prp'] = index['nexp_prp'] # num exposures per slit position
     output_hdr['tr_mode'] = index['tr_mode'] # tracking mode. "FIX" for no tracking
     output_hdr['saa'] = index['saa'] # IN / OUT South Atlantic Anomaly (SAA)
     output_hdr['hlz'] = index['hlz'] # IN / OUT High-Latitude Zone (HLZ)

eispac/data/ref/eis_chianti_lookup_table.txt

@@ -132,6 +132,7 @@
  255.684  Fe VIII   
  171.073  Fe IX     
  177.592  Fe IX     
+ 188.493  Fe IX
  174.531  Fe X      
  175.263  Fe X      
  175.475  Fe X      

eispac/download/eis_obs_struct.py

@@ -73,6 +73,13 @@ def __init__(self, dbfile):
         # Create placeholders
         self.eis_str = []
         self.skipped_obs = []
+        self.unknown_main_row = {'stud_acr':'unknown', 'study_id':-999, 'jop_id':-999, 
+                                 'obstitle':'NO STUDY INFO FOUND! ', 
+                                 'obs_dec':'No study info with same tl_id found within +-12 hrs ', 
+                                 'sci_obj':'?? ', 'target':'unknown'}
+        self.unknown_exp_row = {'filename':' ', 'date_obs':1, 'date_end':2, 
+                                'xcen':-90000, 'ycen':-90000, 'fovx':0.0, 'fovy':0.0, 
+                                'tl_id':0, 'rast_acr':'unknown', 'rast_id':1}
 
     def load_ll(self):
         """Load useful info from line linelist db."""
@@ -169,12 +176,21 @@ def mk_obs_list(self):
             for loop_m_row in main_rows:
                 if primary_db.lower().startswith('main'):
                     # Search the EXPERIMENT DB for info
+                    t_start = loop_m_row['date_obs'] - 43200 # 12 hr BEFORE
+                    t_end = loop_m_row['date_end'] + 43200 # 12 hr AFTER
                     exp_string = ('filename, date_obs, date_end, xcen, ycen,'
                                  +' fovx, fovy, tl_id, rast_acr, rast_id')
                     self.cur.execute('SELECT '+exp_string+' FROM'
-                                    +' eis_experiment WHERE tl_id==?',
-                                    (loop_m_row['tl_id'],))
+                                    +' eis_experiment WHERE tl_id==?'
+                                    +' AND date_obs BETWEEN ? and ?',
+                                    (loop_m_row['tl_id'], t_start, t_end))
                     exp_rows = self.cur.fetchall()
+                    if len(exp_rows) <= 0:
+                        empty_e_row = self.unknown_exp_row
+                        empty_e_row['tl_id'] = loop_m_row['tl_id']
+                        empty_e_row['date_obs'] = loop_m_row['date_obs']
+                        empty_e_row['date_end'] = loop_m_row['date_end']
+                        exp_rows = [empty_e_row]
 
                 for e_row in exp_rows:
                     # Validate rast ID
@@ -243,11 +259,20 @@ def mk_obs_list(self):
                         m_row = loop_m_row
                     elif primary_db.lower().startswith('exp'):
                         # Search the MAIN DB for information
+                        t_start = e_row['date_obs'] - 43200 # 12 hr BEFORE
+                        t_end = e_row['date_end'] + 43200 # 12 hr AFTER
                         main_string = ('stud_acr, study_id, jop_id, obstitle,'
                                       +' obs_dec, sci_obj, target')
                         self.cur.execute('SELECT '+main_string+ ' FROM eis_main'
-                                        +' WHERE tl_id = ?', (e_row['tl_id'],))
-                        m_row, = self.cur.fetchall()
+                                        +' WHERE tl_id = ?'
+                                        +' AND date_obs BETWEEN ? and ?', 
+                                        (e_row['tl_id'], t_start, t_end))
+                        study_rows = self.cur.fetchall()
+                        if len(study_rows) <= 0:
+                            # No matching row found in eis_main!
+                            m_row = self.unknown_main_row
+                        else:
+                            m_row = study_rows[0]
 
                     # Extract, merge, and append the obs info from all rows
                     self.eis_str.append(EIS_Struct(e_row, ll_row, rast_row, m_row))
@@ -276,8 +301,8 @@ def search(self, quiet=False, print_sqlite=False, **kwargs):
             text_cols = ['rast_acr', 'll_acr']
             valid_cols = self.exp_cols
         elif primary_db.lower().startswith('eis_main'):
-            select_cols = ('tl_id, stud_acr, study_id, jop_id, obstitle,'
-                          +' obs_dec, sci_obj, target')
+            select_cols = ('tl_id, date_obs, date_end, stud_acr, study_id,'
+                          +' jop_id, obstitle, obs_dec, sci_obj, target')
             text_cols = ['stud_acr', 'obstitle', 'obs_dec', 'target', 'sci_obj',
                          'join_sb', 'solb_sci', 'eis_sc', 
                          'st_auth', 'observer', 'planner', 'tohbans']

scripts/eis_catalog.py

@@ -160,7 +160,7 @@ def top_menu(self):
         self.download_db.clicked.connect(self.event_download_db)
 
         self.db_source_box = QtWidgets.QComboBox()
-        self.db_source_box.addItems(['NASA (source)', 'NRL (mirror)'])
+        self.db_source_box.addItems(['NRL (source)', 'NASA (mirror)'])
         self.db_source_box.setFixedWidth(self.default_button_width) # or 150
         self.db_source_box.setFont(self.default_font)
 
@@ -198,7 +198,7 @@ def event_download_db(self):
         info = (f'Downloading eis_cat.sqlite.\n'
                 f'   Remote: {db_remote_text}\n'
                 f'   Local: {os.path.abspath(self.dbfile)}\n\n'
-                f'Please wait...')
+                f'Please wait (see console for download progress)...')
         self.info_detail.append(info)
         QtWidgets.QApplication.processEvents() # update gui while user waits
         if self.db_loaded:
@@ -432,9 +432,9 @@ def set_filters(self):
     def event_search(self):
         """Validate and process search request."""
         self.tabs.setCurrentIndex(0) #switch to details tab
+        self.info_detail.clear()
         self.search_info.setText('Found ?? search results')
         self.filter_info.setText('Showing ?? filter matches')
-        self.info_detail.clear()
         if self.db_loaded == False:
             self.info_detail.append('No EIS As-Run Catalog found!\n\n'
                                     +'Please use the "Update Database" '
@@ -622,10 +622,8 @@ def fill_info(self, file):
             info.append(f"{'fovx':<20} {row.fovx}")
             info.append(f"{'fovy':<20} {row.fovy}")
             info.append(f"{'tl_id':<20} {row.tl_id}")
-            info.append(f"{'study_id':<20} {row.study_id}")
-            info.append(f"{'stud_acr':<20} {row.stud_acr}")
-            info.append(f"{'rast_acr':<20} {row.rast_acr}")
-            info.append(f"{'rast_id':<20} {row.rast_id}")
+            info.append(f"{'study_id, stud_acr':<20} {row.study_id}, {row.stud_acr}")
+            info.append(f"{'rast_id, rast_acr':<20} {row.rast_id}, {row.rast_acr}")
             info.append(f"{'jop_id':<20} {row.jop_id}")
             info.append(f"{'obstitle':<20} {row.obstitle}")
             info.append(f"{'obs_dec':<20} {row.obs_dec}")
@@ -638,7 +636,8 @@ def fill_info(self, file):
             info.append(f"{'nexp':<20} {row.nexp}")
             info.append(f"{'exptime':<20} {row.exptime}")
 
-            info.append(f"\n\n{'----- Line List -----':^55}")
+            line_list_title = f"----- Line List (ll_id: {row.ll_id}) -----"
+            info.append(f"\n\n{line_list_title:^55}")
             info.append(f"{'window':<8} {'title':<20} "
                        +f"{'wavemin':<9} {'wavemax':<9} {'width':<5}")
             for i in range(0,len(row.ll_title)):
@@ -683,13 +682,13 @@ def on_finished(self, reply):
 
     def event_update_context_image(self, tab_index):
         """Download context image into memory and update the image tab"""
-        clean_filename = self.selected_file.replace('.gz', '')
-        remote_dir = get_remote_image_dir(clean_filename)
-        context_img_name = 'XRT_'+clean_filename+'.gif'
-        self.context_url = remote_dir+context_img_name
 
         if self.tabs.currentIndex() == 1:
             try:
+                clean_filename = self.selected_file.replace('.gz', '')
+                remote_dir = get_remote_image_dir(clean_filename)
+                context_img_name = 'XRT_'+clean_filename+'.gif'
+                self.context_url = remote_dir+context_img_name
                 self.get_image()
             except:
                 print('   ERROR: context images or server are unavailable.')