Merge branch 'develop' into bad-pixel-monitor

bhilbert4 · Jun 30, 2020 · fac940b · fac940b
2 parents 2f1430c + 5e67b72
commit fac940b
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diff --git a/README.md b/README.md
@@ -145,14 +145,22 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 
 ## Current Development Team
 - Matthew Bourque (INS) [@bourque](https://github.com/bourque)
-- Lauren Chambers (INS) [@laurenmarietta](https://github.com/laurenmarietta)
 - Misty Cracraft (INS) [@cracraft](https://github.com/cracraft)
-- Joe Filippazzo (INS) [@hover2pi](https://github.com/hover2pi)
+- Mike Engesser (INS) [@mengesser](https://github.com/mengesser)
+- Mees Fix (INS) [@mfixstsci](https://github.com/mfixstsci)
 - Bryan Hilbert (INS) [@bilhbert4](https://github.com/bhilbert4)
 - Graham Kanarek (INS) [@gkanarek](https://github.com/gkanarek)
+- Teagan King (INS) [@tnking97](https://github.com/tnking97)
+- Maria Pena-Guerrero [@penaguerrero](https://github.com/penaguerrero)
+- Ben Sunnquist (INS) [@bsunnquist](https://github.com/bsunnquist)
+
+## Past Development Team Members
+- Lauren Chambers (INS) [@laurenmarietta](https://github.com/laurenmarietta)
+- Joe Filippazzo (INS) [@hover2pi](https://github.com/hover2pi)
+- Sara Ogaz (DMD) [@SaOgaz](https://github.com/SaOgaz)
 - Catherine Martlin (INS) [@catherine-martlin](https://github.com/catherine-martlin)
 - Johannes Sahlmann (INS) [@Johannes-Sahlmann](https://github.com/johannes-sahlmann)
-- Ben Sunnquist (INS) [@bsunnquist](https://github.com/bsunnquist)
+
 
 ## Acknowledgments:
 - Faith Abney (DMD)
@@ -194,7 +202,6 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Prem Mishra (ITSD)
 - Don Mueller (ITSD)
 - Maria Antonia Nieto-Santisteban (SEITO)
-- Sara Ogaz (DMD) [@SaOgaz](https://github.com/SaOgaz)
 - Brian O'Sullivan (INS)
 - Joe Pollizzi (JWSTMO)
 - Lee Quick (DMD)

diff --git a/jwql/utils/anomaly_query_config.py b/jwql/utils/anomaly_query_config.py
@@ -0,0 +1,40 @@
+"""Globally defined and used variables for the JWQL query anomaly
+feature. Variables will be re-defined when anomaly query forms are
+submitted.
+
+Authors
+-------
+
+    - Teagan King
+
+
+Use
+---
+    This variables within this module are intended to be directly
+    imported, e.g.:
+    ::
+
+        from jwql.utils.query_config import CHOSEN_INSTRUMENTS
+"""
+
+# Apertures selected by user in query_anomaly_2
+APERTURES_CHOSEN = ["No apertures selected"]
+
+# Anomalies available to select after instruments are selected in query_anomaly
+# Default is all anomalies common to all instruments
+CURRENT_ANOMALIES = ['cosmic_ray_shower', 'diffraction_spike', 'excessive_saturation',
+                     'guidestar_failure', 'persistence', 'other']
+
+# Instruments selected by user in query_anomaly
+INSTRUMENTS_CHOSEN = ["No instruments selected"]
+
+print("INSTRUMENTS_CHOSEN", INSTRUMENTS_CHOSEN)
+
+# Observing modes selected by user
+OBSERVING_MODES_CHOSEN = ["No observing modes selected"]
+
+# Anomalies selected by user in query_anomaly_3
+ANOMALIES_CHOSEN_FROM_CURRENT_ANOMALIES = ["No anomalies selected"]
+
+# Filters selected by user in query_anomaly_2
+FILTERS_CHOSEN = ["No filters selected"]
diff --git a/jwql/utils/constants.py b/jwql/utils/constants.py
@@ -4,6 +4,10 @@
 -------
 
     - Johannes Sahlmann
+    - Matthew Bourque
+    - Bryan Hilbert
+    - Ben Sunnquist
+    - Teagan King
 
 Use
 ---
@@ -47,6 +51,7 @@
                                  '3': [(2, 1032, 4), (0, 1024, 1)],
                                  '4': [(3, 1032, 4), (0, 1024, 1)]}}
 
+# Dictionary describing instruments to which anomalies apply
 ANOMALIES_PER_INSTRUMENT = {
     # anomalies affecting all instruments:
     'cosmic_ray_shower': ['fgs', 'miri', 'nircam', 'niriss', 'nirspec'],
@@ -92,6 +97,17 @@
                   'nirspec': ['NRS_AUTOFLAT', 'NRS_LAMP'],
                   'fgs': ['FGS_INTFLAT']}
 
+FILTERS_PER_INSTRUMENT = {'miri': ['F560W', 'F770W', 'F1000W', 'F1065C', 'F1130W', 'F1140C', 'F1280W',
+                                   'F1500W', 'F1550C', 'F1800W', 'F2100W', 'F2300C', 'F2550W'],
+                          'nircam': ['F070W', 'F090W', 'F115W', 'F140M', 'F150W', 'F150W2', 'F162M',
+                                     'F164N', 'F182M', 'F187N', 'F200W', 'F210M', 'F212N', 'F250M',
+                                     'F277W', 'F300M', 'F322W2', 'F323N', 'F335M', 'F356W', 'F360M',
+                                     'F405N', 'F410M', 'F430M', 'F444W', 'F460M', 'F466N', 'F470N',
+                                     'F480M'],
+                          'niriss': ['F090W', 'F115W', 'F140M', 'F150W', 'F185M', 'F200W', 'F227W',
+                                     'F356W', 'F380M', 'F430M', 'F444W', 'F480M'],
+                          'nirspec': ['CLEAR', 'F070LP', 'F100LP', 'F170LP', 'F290LP']}
+
 FOUR_AMP_SUBARRAYS = ['WFSS128R', 'WFSS64R', 'WFSS128C', 'WFSS64C']
 
 # Names of full-frame apertures for all instruments
@@ -111,6 +127,7 @@
 # Possible suffix types for guider exposures
 GUIDER_SUFFIX_TYPES = ['stream', 'stacked_uncal', 'image_uncal', 'stacked_cal', 'image_cal']
 
+# Instrument monitor database tables
 INSTRUMENT_MONITOR_DATABASE_TABLES = {
     'dark_monitor': ['<instrument>_dark_dark_current', '<instrument>_dark_pixel_stats', '<instrument>_dark_query_history'],
     'bad_pixel_monitor': ['<instrument>_bad_pixel_stats', '<instrument>_bad_pixel_query_history']}
@@ -193,6 +210,15 @@
 # Possible suffix types for AMI files
 NIRISS_AMI_SUFFIX_TYPES = ['amiavg', 'aminorm', 'ami']
 
+# Dictionary of observing modes available for each instrument
+OBSERVING_MODE_PER_INSTRUMENT = {'miri': ['Imaging', '4QPM Coronagraphic Imaging',
+                                          'Lyot Coronagraphic Imaging', 'LRS', 'MRS'],
+                                 'nircam': ['Imaging', 'Coronagraphic Imaging', 'WFSS',
+                                            'Time-Series Imaging', 'Grism Time Series'],
+                                 'niriss': ['WFSS', 'SOSS', 'AMI', 'Imaging'],
+                                 'nirspec': ['Multi-Object Spectroscopy', 'IFU Spectroscopy',
+                                             'Fixed Slit Spectroscopy', 'Bright Object Time Series']}
+
 SUBARRAYS_ONE_OR_FOUR_AMPS = ['SUBGRISMSTRIPE64', 'SUBGRISMSTRIPE128', 'SUBGRISMSTRIPE256']
 
 # Possible suffix types for time-series exposures

diff --git a/jwql/website/apps/jwql/api_views.py b/jwql/website/apps/jwql/api_views.py
@@ -26,6 +26,7 @@
 -------
 
     - Matthew Bourque
+    - Teagan King
 
 Use
 ---
@@ -56,7 +57,6 @@
 from .data_containers import get_thumbnails_by_instrument
 from .data_containers import get_thumbnails_by_proposal
 from .data_containers import get_thumbnails_by_rootname
-from .oauth import auth_required
 
 
 def all_proposals(request):
@@ -216,7 +216,7 @@ def thumbnails_by_instrument(request, inst):
         Incoming request from the webpage
     inst : str
         The instrument of interest.  The name of the instrument must
-        mach one of the following: (``nircam``, ``NIRCam``, ``niriss``,
+        match one of the following: (``nircam``, ``NIRCam``, ``niriss``,
         ``NIRISS``, ``nirspec``, ``NIRSpec``, ``miri``, ``MIRI``,
         ``fgs``, ``FGS``).
 

diff --git a/jwql/website/apps/jwql/data_containers.py b/jwql/website/apps/jwql/data_containers.py
@@ -10,6 +10,7 @@
 
     - Lauren Chambers
     - Matthew Bourque
+    - Teagan King
 
 Use
 ---
@@ -485,7 +486,8 @@ def get_filenames_by_rootname(rootname):
     Parameters
     ----------
     rootname : str
-        The rootname of interest (e.g. ``jw86600008001_02101_00007_guider2``).
+        The rootname of interest (e.g.
+        ``jw86600008001_02101_00007_guider2``).
 
     Returns
     -------
@@ -725,7 +727,8 @@ def get_preview_images_by_rootname(rootname):
     Parameters
     ----------
     rootname : str
-        The rootname of interest (e.g. ``jw86600008001_02101_00007_guider2``).
+        The rootname of interest (e.g.
+        ``jw86600008001_02101_00007_guider2``).
 
     Returns
     -------
@@ -792,7 +795,48 @@ def get_proposal_info(filepaths):
 
     return proposal_info
 
+
+def get_thumbnails_all_instruments(instruments):
+    """Return a list of thumbnails available in the filesystem for all
+    instruments given requested parameters.
+
+    Returns
+    -------
+    thumbnails : list
+        A list of thumbnails available in the filesystem for the
+        given instrument.
+    """
+
+    # Make sure instruments are of the proper format (e.g. "Nircam")
+    thumbnail_list = []
+    for inst in instruments:  # JWST_INSTRUMENT_NAMES:
+        instrument = inst[0].upper()+inst[1:].lower()
 
+        ### adjust query based on request
+
+        # Query MAST for all rootnames for the instrument
+        service = "Mast.Jwst.Filtered.{}".format(instrument)
+        params = {"columns": "filename, expstart, filter, readpatt, date_beg, date_end, apername, exp_type",
+                  "filters": [{"paramName": "expstart",
+                  "values": [{"min": 57404.04, "max": 57404.07}], }]}
+        response = Mast.service_request_async(service, params)
+        results = response[0].json()['data']
+
+        # Parse the results to get the rootnames
+        filenames = [result['filename'].split('.')[0] for result in results]
+
+        # Get list of all thumbnails
+        thumbnails = glob.glob(os.path.join(THUMBNAIL_FILESYSTEM, '*', '*.thumb'))
+
+    thumbnail_list.extend(thumbnails)
+
+    # Get subset of preview images that match the filenames
+    thumbnails = [os.path.basename(item) for item in thumbnail_list if
+                  os.path.basename(item).split('_integ')[0] in filenames]
+
+    return thumbnails
+
+
 def get_jwqldb_table_view_components(request):
     """Renders view for JWQLDB table viewer.
 
@@ -904,7 +948,8 @@ def get_thumbnails_by_rootname(rootname):
     Parameters
     ----------
     rootname : str
-        The rootname of interest (e.g. ``jw86600008001_02101_00007_guider2``).
+        The rootname of interest (e.g.
+        ``jw86600008001_02101_00007_guider2``).
 
     Returns
     -------