Merge branch 'develop' into order_sync

pypeit · Aug 30, 2024 · 1fed401 · 1fed401
2 parents 0665fee + bd77c38
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diff --git a/deprecated/arc_old.py b/deprecated/arc_old.py
@@ -855,3 +855,53 @@ def saturation_mask(a, satlevel):
 
     return mask.astype(int)
 
+def mask_around_peaks(spec, inbpm):
+    """
+    Find peaks in the input spectrum and mask pixels around them.
+
+    All pixels to the left and right of a peak is masked until
+    a pixel has a lower value than the adjacent pixel. At this
+    point, we assume that spec has reached the noise level.
+
+    Parameters
+    ----------
+    spec: `numpy.ndarray`_
+        Spectrum (1D array) in counts
+    inbpm: `numpy.ndarray`_
+        Input bad pixel mask
+
+    Returns
+    -------
+    outbpm: `numpy.ndarray`_
+        Bad pixel mask with pixels around peaks masked
+    """
+    # Find the peak locations
+    pks = detect_peaks(spec)
+
+    # Initialise some useful variables and the output bpm
+    xarray = np.arange(spec.size)
+    specdiff = np.append(np.diff(spec), 0.0)
+    outbpm = inbpm.copy()
+
+    # Loop over the peaks and mask pixels around them
+    for i in range(len(pks)):
+        # Find all pixels to the left of the peak that are above the noise level
+        wl = np.where((xarray <= pks[i]) & (specdiff > 0.0))[0]
+        ww = (pks[i]-wl)[::-1]
+        # Find the first pixel to the left of the peak that is below the noise level
+        nmask = np.where(np.diff(ww) > 1)[0]
+        if nmask.size != 0 and nmask[0] > 5:
+            # Mask all pixels to the left of the peak
+            mini = max(0,wl.size-nmask[0]-1)
+            outbpm[wl[mini]:pks[i]] = True
+        # Find all pixels to the right of the peak that are above the noise level
+        ww = np.where((xarray >= pks[i]) & (specdiff < 0.0))[0]
+        # Find the first pixel to the right of the peak that is below the noise level
+        nmask = np.where(np.diff(ww) > 1)[0]
+        if nmask.size != 0 and nmask[0] > 5:
+            # Mask all pixels to the right of the peak
+            maxi = min(nmask[0], ww.size)
+            outbpm[pks[i]:ww[maxi]+2] = True
+    # Return the output bpm
+    return outbpm
+
diff --git a/doc/api/pypeit.spectrographs.aat_uhrf.rst b/doc/api/pypeit.spectrographs.aat_uhrf.rst
@@ -0,0 +1,8 @@
+pypeit.spectrographs.aat\_uhrf module
+=====================================
+
+.. automodule:: pypeit.spectrographs.aat_uhrf
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.spectrographs.rst b/doc/api/pypeit.spectrographs.rst
@@ -7,6 +7,7 @@ Submodules
 .. toctree::
    :maxdepth: 4
 
+   pypeit.spectrographs.aat_uhrf
    pypeit.spectrographs.bok_bc
    pypeit.spectrographs.gemini_flamingos
    pypeit.spectrographs.gemini_gmos

diff --git a/doc/cookbook.rst b/doc/cookbook.rst
@@ -70,7 +70,8 @@ what we recommend:
  - We will refer to that folder as ``RAWDIR``
 
 The raw images can be gzip-compressed, although this means opening files will be
-slower.
+slower.  See :ref:`setup-file-searching` for specific comments about the files
+in your raw directory.
 
 A word on calibration data
 --------------------------

diff --git a/doc/help/pypeit_cache_github_data.rst b/doc/help/pypeit_cache_github_data.rst
@@ -9,7 +9,7 @@
     Script to download/cache PypeIt github data
     
     positional arguments:
-      spectrograph          A valid spectrograph identifier: bok_bc,
+      spectrograph          A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
                             gemini_gmos_north_ham_ns, gemini_gmos_south_ham,

diff --git a/doc/help/pypeit_chk_for_calibs.rst b/doc/help/pypeit_chk_for_calibs.rst
@@ -13,7 +13,7 @@
     options:
       -h, --help            show this help message and exit
       -s SPECTROGRAPH, --spectrograph SPECTROGRAPH
-                            A valid spectrograph identifier: bok_bc,
+                            A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
                             gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
@@ -35,8 +35,11 @@
                             vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
                             wht_isis_blue, wht_isis_red (default: None)
       -e EXTENSION, --extension EXTENSION
-                            File extension; compression indicators (e.g. .gz) not
-                            required. (default: .fits)
+                            File extension to use. Must include the period (e.g.,
+                            ".fits") and it must be one of the allowed extensions
+                            for this spectrograph. If None, root directory will be
+                            searched for all files with any of the allowed
+                            extensions. (default: None)
       --save_setups         If not toggled, remove setup_files/ folder and its
                             files. (default: False)
     
diff --git a/doc/help/pypeit_obslog.rst b/doc/help/pypeit_obslog.rst
@@ -10,7 +10,7 @@
     using PypeItMetaData.
     
     positional arguments:
-      spec                  A valid spectrograph identifier: bok_bc,
+      spec                  A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
                             gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
@@ -75,8 +75,11 @@
       -s SORT, --sort SORT  Metadata keyword (pypeit-specific) to use to sort the
                             output table. (default: mjd)
       -e EXTENSION, --extension EXTENSION
-                            File extension; compression indicators (e.g. .gz) not
-                            required. (default: .fits)
+                            File extension to use. Must include the period (e.g.,
+                            ".fits") and it must be one of the allowed extensions
+                            for this spectrograph. If None, root directory will be
+                            searched for all files with any of the allowed
+                            extensions. (default: None)
       -d OUTPUT_PATH, --output_path OUTPUT_PATH
                             Path to top-level output directory. (default: current
                             working directory)

diff --git a/doc/help/pypeit_ql.rst b/doc/help/pypeit_ql.rst
@@ -17,7 +17,7 @@
     Script to produce quick-look PypeIt reductions
     
     positional arguments:
-      spectrograph          A valid spectrograph identifier: bok_bc,
+      spectrograph          A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
                             gemini_gmos_north_ham_ns, gemini_gmos_south_ham,

diff --git a/doc/help/pypeit_setup.rst b/doc/help/pypeit_setup.rst
@@ -11,7 +11,7 @@
     options:
       -h, --help            show this help message and exit
       -s SPECTROGRAPH, --spectrograph SPECTROGRAPH
-                            A valid spectrograph identifier: bok_bc,
+                            A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
                             gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
@@ -39,8 +39,11 @@
                             --extension option to set the types of files to search
                             for. (default: current working directory)
       -e EXTENSION, --extension EXTENSION
-                            File extension; compression indicators (e.g. .gz) not
-                            required. (default: .fits)
+                            File extension to use. Must include the period (e.g.,
+                            ".fits") and it must be one of the allowed extensions
+                            for this spectrograph. If None, root directory will be
+                            searched for all files with any of the allowed
+                            extensions. (default: None)
       -d OUTPUT_PATH, --output_path OUTPUT_PATH
                             Path to top-level output directory. (default: current
                             working directory)

diff --git a/doc/help/pypeit_trace_edges.rst b/doc/help/pypeit_trace_edges.rst
@@ -26,16 +26,16 @@
                             default mosaic. (default: None)
       -s SPECTROGRAPH, --spectrograph SPECTROGRAPH
                             A valid spectrograph identifier, which is only used if
-                            providing files directly: bok_bc, gemini_flamingos1,
-                            gemini_flamingos2, gemini_gmos_north_e2v,
-                            gemini_gmos_north_ham, gemini_gmos_north_ham_ns,
-                            gemini_gmos_south_ham, gemini_gnirs_echelle,
-                            gemini_gnirs_ifu, gtc_maat, gtc_osiris, gtc_osiris_plus,
-                            jwst_nircam, jwst_nirspec, keck_deimos, keck_esi,
-                            keck_hires, keck_kcrm, keck_kcwi, keck_lris_blue,
-                            keck_lris_blue_orig, keck_lris_red, keck_lris_red_mark4,
-                            keck_lris_red_orig, keck_mosfire, keck_nires,
-                            keck_nirspec_high, keck_nirspec_high_old,
+                            providing files directly: aat_uhrf, bok_bc,
+                            gemini_flamingos1, gemini_flamingos2,
+                            gemini_gmos_north_e2v, gemini_gmos_north_ham,
+                            gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
+                            gemini_gnirs_echelle, gemini_gnirs_ifu, gtc_maat,
+                            gtc_osiris, gtc_osiris_plus, jwst_nircam, jwst_nirspec,
+                            keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
+                            keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
+                            keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
+                            keck_nires, keck_nirspec_high, keck_nirspec_high_old,
                             keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
                             lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
                             magellan_fire, magellan_fire_long, magellan_mage,

diff --git a/doc/help/pypeit_view_fits.rst b/doc/help/pypeit_view_fits.rst
@@ -9,7 +9,7 @@
     View FITS files with ginga
     
     positional arguments:
-      spectrograph         A valid spectrograph identifier: bok_bc,
+      spectrograph         A valid spectrograph identifier: aat_uhrf, bok_bc,
                            gemini_flamingos1, gemini_flamingos2,
                            gemini_gmos_north_e2v, gemini_gmos_north_ham,
                            gemini_gmos_north_ham_ns, gemini_gmos_south_ham,

diff --git a/doc/help/run_pypeit.rst b/doc/help/run_pypeit.rst
@@ -7,11 +7,11 @@
     ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.16.1.dev336+gdf3013372.d20240827[0m
     ##  
     ##  Available spectrographs include:
-    ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,
-    ##   gemini_gmos_north_ham, gemini_gmos_north_ham_ns,
-    ##   gemini_gmos_south_ham, gemini_gnirs_echelle, gemini_gnirs_ifu,
-    ##   gtc_maat, gtc_osiris, gtc_osiris_plus, jwst_nircam, jwst_nirspec,
-    ##   keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
+    ##   aat_uhrf, bok_bc, gemini_flamingos1, gemini_flamingos2,
+    ##   gemini_gmos_north_e2v, gemini_gmos_north_ham,
+    ##   gemini_gmos_north_ham_ns, gemini_gmos_south_ham, gemini_gnirs_echelle,
+    ##   gemini_gnirs_ifu, gtc_maat, gtc_osiris, gtc_osiris_plus, jwst_nircam,
+    ##   jwst_nirspec, keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
     ##   keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
     ##   keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire, keck_nires,
     ##   keck_nirspec_high, keck_nirspec_high_old, keck_nirspec_low, lbt_luci1,

diff --git a/doc/include/inst_detector_table.rst b/doc/include/inst_detector_table.rst
@@ -1,6 +1,7 @@
 ============================  ===  ========  ========  ========  ========  ==========================  ======================  ========  ========  ============  =========  ==========
 Instrument                    Det  specaxis  specflip  spatflip  namp      gain                        RN                      darkcurr  min       sat           nonlinear  platescale
 ============================  ===  ========  ========  ========  ========  ==========================  ======================  ========  ========  ============  =========  ==========
+``aat_uhrf``                  1    0         False     False     1         1.0                         0.0                     0.0       -1.0e+10  65535.0       0.7600     0.0500    
 ``bok_bc``                    1    1         False     False     1         1.5                         3.0                     5.4       -1.0e+10  65535.0       1.0000     0.2000    
 ``gemini_flamingos1``         1    0         False     False     1         3.8                         6.0                     1080.0    -1.0e+10  320000.0      0.8750     0.1500    
 ``gemini_flamingos2``         1    0         True      False     1         4.44                        5.0                     1800.0    -1.0e+10  700000.0      1.0000     0.1787    

diff --git a/doc/include/spectrographs_table.rst b/doc/include/spectrographs_table.rst
@@ -1,6 +1,7 @@
 ========================  ============================================================================  =========  ============  ===============================================================================================================================  =========  =========  =========  ===============================================================================================
 ``PypeIt`` Name           ``PypeIt`` Class                                                              Telescope  Camera        URL                                                                                                                              Pipeline   Supported  QL Tested  Comments                                                                                       
 ========================  ============================================================================  =========  ============  ===============================================================================================================================  =========  =========  =========  ===============================================================================================
+aat_uhrf                  :class:`~pypeit.spectrographs.aat_uhrf.AATUHRFSpectrograph`                   AAT        UHRF          `Link <https://aat.anu.edu.au/science/instruments/decomissioned/uhrf/overview>`__                                                MultiSlit  True       False                                                                                                     
 bok_bc                    :class:`~pypeit.spectrographs.bok_bc.BokBCSpectrograph`                       BOK        BC            `Link <http://james.as.arizona.edu/~psmith/90inch/90inch.html>`__                                                                MultiSlit  True       False      Bok B&C spectrometer                                                                           
 gemini_flamingos1         :class:`~pypeit.spectrographs.gemini_flamingos.GeminiFLAMINGOS1Spectrograph`  GEMINI-S   FLAMINGOS     `Link <https://www.gemini.edu/instrumentation/flamingos-2>`__                                                                    MultiSlit  False      False                                                                                                     
 gemini_flamingos2         :class:`~pypeit.spectrographs.gemini_flamingos.GeminiFLAMINGOS2Spectrograph`  GEMINI-S   FLAMINGOS     `Link <https://www.gemini.edu/instrumentation/flamingos-2>`__                                                                    MultiSlit  True       False      Flamingos-2 NIR spectrograph