measureIQ calls added in GNIRS and F2 QA recipes, autoredux changes (#…

…411)

* F2/GNIRS LS Spect work/autoredux updates to support them

* adding SECTION constant and passing down to avoid doublepeak issues for certain F2

* ensuring text widgets get initialized on creation, needed for apertures interactive (found during work)

* fix AstroDataF2.camera() logic to not require pixel_scale() (so it works on 1D spectra)

* pulled F2 camera fix from CS, simplifying paths for 1D requests for 2D functionality to return None

* inverted section parsing logic to clean things up

* handling None string in Section parse

* removing imports that are no longer needed

astrodata/utils.py

@@ -266,6 +266,9 @@ def from_shape(value):
     @staticmethod
     def from_string(value):
         """The inverse of __str__, produce a Section object from a string"""
+        # if we were sent None, return None
+        if value is None:
+            return None
         return Section(*[y for x in value.strip("[]").split(",")
                          for start, end in [x.split(":")]
                          for y in (None if start == '' else int(start)-1,

gemini_instruments/gemini/adclass.py

@@ -9,6 +9,7 @@
 import math
 import datetime
 import dateutil.parser
+from itertools import chain
 
 import numpy as np
 
@@ -384,17 +385,23 @@ def _dec(self):
 
     def _parse_section(self, keyword, pretty):
         try:
-            value_filter = (str if pretty else Section.from_string)
+            value_filter = lambda x: (x.asIRAFsection() if pretty else x)
             process_fn = lambda x: (None if x is None else value_filter(x))
             # Dummy keyword FULLFRAME returns shape of full data array
             if keyword == 'FULLFRAME':
+                def _encode_shape(shape):
+                    if not shape:
+                        return None
+                    return Section(*chain.from_iterable([(0, npix) for npix in shape[::-1]]))
                 if self.is_single:
-                    sections = '[1:{1},1:{0}]'.format(*self.shape)
+                    sections = _encode_shape(self.shape)
                 else:
-                    sections = ['[1:{1},1:{0}]'.format(*ext.shape)
-                                for ext in self]
+                    sections = [_encode_shape(ext.shape) for ext in self]
             else:
-                sections = self.hdr.get(keyword)
+                if self.is_single:
+                    sections = Section.from_string(self.hdr.get(keyword))
+                else:
+                    sections = [Section.from_string(sec) if sec is not None else None for sec in self.hdr.get(keyword)]
             if self.is_single:
                 return process_fn(sections)
             else:
@@ -2151,9 +2158,11 @@ def empirical_pixel_scale(ext):
 
         pixel_scale_list = []
         for ext in self:
+            if len(ext.shape) < 2:
+                return None
             try:
                 pixel_scale_list.append(3600 * np.sqrt(abs(np.linalg.det(ext.wcs.forward_transform['cd_matrix'].matrix))))
-            except (IndexError, AttributeError):
+            except (IndexError, AttributeError) as iae:
                 scale = empirical_pixel_scale(ext)
                 if scale is not None:
                     pixel_scale_list.append(scale)

geminidr/core/primitives_spect.py

@@ -2284,8 +2284,11 @@ def findApertures(self, adinputs=None, **params):
                                              placeholders={"section": "e.g. 100:900,1500:2000"})
 
                     # pass "direction" purely for logging purposes
+                    filename = ad.filename
+                    if not filename:
+                        filename = ad.orig_filename
                     locations, all_limits = interactive_find_source_apertures(
-                        ext_oriented, ui_params=ui_params, **aper_params,
+                        ext_oriented, ui_params=ui_params, filename=filename, **aper_params,
                         direction="column" if dispaxis == 0 else "row")
                 else:
                     locations, all_limits, _, _ = tracing.find_apertures(

geminidr/core/primitives_visualize.py

@@ -594,7 +594,7 @@ def plotSpectraForQA(self, adinputs=None, **params):
                 stack_size = 1
 
             group_id = ad.group_id().split('_[')[0]
-            group_id += ad.group_id().split(']')[1]
+            group_id += ad.group_id().split(']')[-1]
 
             offset = (ad.telescope_y_offset() if ad.dispersion_axis()[0] == 1
                       else ad.telescope_x_offset())

geminidr/f2/recipes/qa/recipes_LS_SPECT.py

@@ -2,8 +2,11 @@
 Recipes available to data with tags ['F2', 'SPECT', LS'].
 Default is "reduceScience".
 """
+from time import sleep
+
 recipe_tags = {'F2', 'SPECT', 'LS'}
 
+
 def reduceScience(p):
     """
     To be updated as development continues: This recipe processes F2 longslit 
@@ -20,6 +23,7 @@ def reduceScience(p):
     p.ADUToElectrons()
     p.addVAR(poisson_noise=True, read_noise=True)
     p.darkCorrect()
+    p.measureIQ(display=True)
     p.flatCorrect()
     p.attachWavelengthSolution()
     p.addToList(purpose='forSky')
@@ -48,7 +52,7 @@ def reduceScience(p):
     p.measureIQ(display=True)
     p.traceApertures()
     p.extractSpectra()
-    p.plotspectraForQA()
+    p.plotSpectraForQA()
 
 
 _default = reduceScience

geminidr/gnirs/recipes/qa/recipes_LS_SPECT.py

@@ -4,6 +4,7 @@
 """
 recipe_tags = {'GNIRS', 'SPECT', 'LS'}
 
+
 def reduceScience(p):
     """
     To be updated as development continues: This recipe processes GNIRS longslit 
@@ -19,6 +20,7 @@ def reduceScience(p):
     # p.nonlinearityCorrect() # non-linearity correction tbd 
     p.ADUToElectrons()
     p.addVAR(poisson_noise=True, read_noise=True)
+    p.measureIQ(display=True)
     p.flatCorrect()
     p.attachWavelengthSolution()
     p.addToList(purpose='forSky')
@@ -37,6 +39,7 @@ def reduceScience(p):
     # The GUI polls for new data every 3 seconds.  The next steps can be
     # quicker than that leading to the second plotSpectra to hijack this one.
     # Hijacking issues were highlighted in integration tests.
+    from time import sleep
     sleep(3)
 
     # continuing with the main stream of 2D pre-stack

geminidr/interactive/fit/aperture.py

@@ -999,7 +999,7 @@ def result(self):
         return np.array(locations), limits
 
 
-def interactive_find_source_apertures(ext, ui_params=None, **kwargs):
+def interactive_find_source_apertures(ext, ui_params=None, filename=None, **kwargs):
     """
     Perform an interactive find of source apertures with the given initial
     parameters.
@@ -1012,6 +1012,10 @@ def interactive_find_source_apertures(ext, ui_params=None, **kwargs):
 
     """
     model = FindSourceAperturesModel(ext, **kwargs)
-    fsav = FindSourceAperturesVisualizer(model, ui_params=ui_params, filename_info=ext.filename)
+    if not filename:
+        filename = ext.filename
+    if not filename and hasattr(ext, "orig_filename"):
+        filename = ext.orig_filename
+    fsav = FindSourceAperturesVisualizer(model, ui_params=ui_params, filename_info=filename)
     interactive_fitter(fsav)
     return fsav.result()

geminidr/interactive/fit/fit1d.py

@@ -138,6 +138,7 @@ def __init__(self, fitting_parameters, domain, x=None, y=None, weights=None,
 
         self.fitting_parameters = fitting_parameters
         self.domain = domain
+        self.fit = initial_fit
         if len(x) == 0:
             self.fit = initial_fit
         self.listeners = listeners
@@ -390,6 +391,9 @@ def perform_fit(self, *args):
                 if rank >= fitparms["order"]:
                     self.quality = FitQuality.GOOD
                     self.fit = new_fit
+                elif self.fit is None:
+                    self.quality = FitQuality.BAD
+                    self.fit = new_fit
                 else:
                     # Modify the fit_1D object with a shift by ugly hacking
                     offset = np.mean(self.y[goodpix] - self.evaluate(self.x[goodpix]))

geminidr/interactive/interactive.py

@@ -634,12 +634,14 @@ def _cb_handler(cbkey, val):
                         title = params.titles[key]
                     else:
                         title = _title_from_field(field)
+                    val = self.ui_params.values.get(key, "")
                     widget = TextInput(title=title,
                                        min_width=100,
                                        max_width=256,
                                        width_policy="fit",
                                        placeholder=params.placeholders[key]
-                                       if key in params.placeholders else None)
+                                       if key in params.placeholders else None,
+                                       value=val)
 
                     class TextHandler:
                         def __init__(self, key, extras, fn):

gempy/gemini/gemini_tools.py

@@ -1204,7 +1204,7 @@ def fit_continuum(ad):
             # are a multiple of 512 pixels. We do this because the data are
             # unlikely to have gone through traceApertures() so we can't
             # account for curvature in the spectral trace.
-            hwidth = 512 // spectral_bin
+            hwidth = min(512 // spectral_bin, dispersed_length // 2)
             centers = [i*hwidth for i in range(1, dispersed_length // hwidth, 1)]
         spectral_slices = [slice(center-hwidth, center+hwidth) for center in centers]
 

gempy/library/fitsverify.py

@@ -40,8 +40,9 @@ def fitsverify(filename):
     subproc = subprocess.Popen([FITSVERIFY_BIN, filename], stdout=subprocess.PIPE,
                           stderr=subprocess.PIPE)
     (stdoutstring, stderrstring) = subproc.communicate()
-
+   
     stdoutstring += stderrstring
+
     # Check to see if we got a not a fits file situation
     nfmatch = NFRE.search(stdoutstring.decode('utf-8'))
     if nfmatch: