added full test

.gitignore

@@ -160,3 +160,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Data files and pipeline output
+*.bin
+*.h5

mkidpipeline/definitions.py

@@ -364,11 +364,11 @@ def _metadata(self):
         try:
             d.update(dict(E_CXREFX=self.wcscal.conex_ref[0], E_CXREFY=self.wcscal.conex_ref[1],
                           E_PREFX=self.wcscal.pixel_ref[0], E_PREFY=self.wcscal.pixel_ref[1],
-                          E_PLTSCL=self.wcscal.platescale if self.wcscal.platescale else self.photontable.query_header(
+                          E_PLTSCL=self.wcscal.platescale if self.wcscal.platescale is not None else self.photontable.query_header(
                               'E_PLTSCL'),
-                          E_DPDCX=self.wcscal.dp_dcx if self.wcscal.dp_dcx else self.photontable.query_header(
+                          E_DPDCX=self.wcscal.dp_dcx if self.wcscal.dp_dcx is not None else self.photontable.query_header(
                               'E_DPDCX'),
-                          E_DPDCY=self.wcscal.dp_dcy if self.wcscal.dp_dcy else self.photontable.query_header(
+                          E_DPDCY=self.wcscal.dp_dcy if self.wcscal.dp_dcy is not None else self.photontable.query_header(
                               'E_DPDCY')))
         except (AttributeError, KeyError) as error:
             pass

mkidpipeline/utils/wavecal_models.py

@@ -269,8 +269,16 @@ def fit(self, guess):
                                                          weights=1 / np.sqrt(variance), scale_covar=False,
                                                          nan_policy='propagate')
             # find the linear amplitude coefficients
-            amplitudes = self._reduced_model.eval(fit_result.params, x=x, y=y, variance=variance,
-                                                  return_amplitudes=True)
+            amplitudes = self._reduced_model.func(
+                **self._reduced_model.make_funcargs(
+                    fit_result.params, {
+                        'x': x,
+                        'y': y,
+                        'variance': variance,
+                        'return_amplitudes': True
+                    }
+                )
+            )
             # set the minimum amplitude to be 0 for the full fit
             for amplitude in amplitudes.values():
                 amplitude.set(min=0)

tests/data/hip109427-subset/20201006/logs/dither_202010070311.log

@@ -0,0 +1,5 @@
+2020-10-06 19:32:36,481 Dither Path: (0.1, -0.4) --> (-0.3, 0.2), 6 steps 25.0 seconds
+	starts=[1602047817.008426, 1602047843.0487542, 1602047869.057722, 1602047895.0989745, 1602047921.027141, 1602047946.9576638, 1602047973.1737182, 1602047999.326166, 1602048025.351133, 1602048051.327375, 1602048077.3532414, 1602048103.32894, 1602048129.8022091, 1602048155.7942092, 1602048181.819404, 1602048207.8119497, 1602048233.7745168, 1602048259.7029226, 1602048285.9824896, 1602048312.0880666, 1602048338.447823, 1602048364.5527227, 1602048390.5130281, 1602048416.5059514, 1602048442.7548149, 1602048468.7794, 1602048494.8036757, 1602048520.7800586, 1602048546.7407908, 1602048572.7495456, 1602048598.9976673, 1602048625.0391998, 1602048651.0160012, 1602048676.9604523, 1602048702.9853165, 1602048729.026347]
+	ends=[1602047842.0098252, 1602047868.0501366, 1602047894.059312, 1602047920.099934, 1602047946.0284781, 1602047971.958183, 1602047998.174311, 1602048024.327056, 1602048050.3521876, 1602048076.3278682, 1602048102.3537316, 1602048128.3302114, 1602048154.8035254, 1602048180.7953146, 1602048206.8207395, 1602048232.8132064, 1602048258.777208, 1602048284.7035637, 1602048310.9838514, 1602048337.088304, 1602048363.4486434, 1602048389.5543034, 1602048415.5146558, 1602048441.5078225, 1602048467.7558453, 1602048493.7809784, 1602048519.8052933, 1602048545.782158, 1602048571.7416408, 1602048597.7514176, 1602048623.9986145, 1602048650.0410624, 1602048676.0174, 1602048701.9615557, 1602048727.9862337, 1602048754.0277302]
+	path=[(0.1, -0.4), (0.1, -0.28), (0.1, -0.16), (0.1, -0.04), (0.1, 0.08), (0.1, 0.2), (0.02, -0.4), (0.02, -0.28), (0.02, -0.16), (0.02, -0.04), (0.02, 0.08), (0.02, 0.2), (-0.06, -0.4), (-0.06, -0.28), (-0.06, -0.16), (-0.06, -0.04), (-0.06, 0.08), (-0.06, 0.2), (-0.14, -0.4), (-0.14, -0.28), (-0.14, -0.16), (-0.14, -0.04), (-0.14, 0.08), (-0.14, 0.2), (-0.22, -0.4), (-0.22, -0.28), (-0.22, -0.16), (-0.22, -0.04), (-0.22, 0.08), (-0.22, 0.2), (-0.3, -0.4), (-0.3, -0.28), (-0.3, -0.16), (-0.3, -0.04), (-0.3, 0.08), (-0.3, 0.2)]
+

tests/data/hip109427-subset/data.yaml

@@ -0,0 +1,48 @@
+- !MKIDWavecal
+  name: wavecal0  # A name
+  data: # List of MKIDTimerange named like 950 nm
+  - !MKIDTimerange 
+    name: 850.0 nm  # A name
+    start: 1602040829.0 # The start unix time, float ok, rounded down for H5 creation.
+    stop:  1602040834.0 # A stop unit time, float ok. If not specified duration must be
+    header: # A dictionary of fits header key overrides.
+      laser: on  # !UNKNOWN MEC HEADER KEY!
+      other: fits_key # !UNKNOWN MEC HEADER KEY!
+  - !MKIDTimerange
+    name: 1.1 um  # A name
+    start: 1602040979.0 # The start unix time, float ok, rounded down for H5 creation.
+    stop:  1602041084.0 # A stop unit time, float ok. If not specified duration must be
+    header: {} # A dictionary of fits header key overrides.
+  - !MKIDTimerange
+    name: 13750.0 Angstrom  # A name
+    start: 1602041119.0 # The start unix time, float ok, rounded down for H5 creation.
+    stop:  1602041124.0 # A stop unit time, float ok. If not specified duration must be
+    header: {} # A dictionary of fits header key overrides.
+- !MKIDFlatcal
+  name: flatcal0  # A name
+  data: wavecal0 # An MKIDObservation (for a whitelight flat) or an MKIDWavedata (or name) for a lasercal flat
+  wavecal_duration: 3.0 # Number of seconds of the wavecal to use, float ok. Required if using wavecal
+  wavecal_offset: 1.1 # An offset in seconds (>=1) from the start of the wavecal timerange. Required if not ob
+  lincal: false # Apply lincal to h5s 
+  pixcal: true # Apply pixcal to data 
+  cosmiccal: false # Apply cosmiccal to data 
+- !MKIDWCSCal
+  name: wcscal0  # A name
+  data: 10.4 mas # MKIDObservation, MKIDDither, or platescale (e.g. 10 mas)
+  pixel_ref: # The pixel position of the target centroid when on axis and the conex is at conex_ref
+  - 107
+  - 46
+  conex_ref: # The conex (x,y) position, [0, 1.0], when the target is at pixel_ref 
+  - -0.16
+  - -0.4
+  source_locs: [] # The RA/DEC coordinates of the sources in the image 
+- !MKIDDither
+  name: dither0  # A name
+  data: 1602047815.0 # A list of !sob composing the dither, a unix time that falls within the range of a dither log in paths.data, or a fully qualified legacy (starttimes, endtimes, xpos,ypos) dither file.
+  wavecal: wavecal0 # A MKIDWavedata or name of the same
+  flatcal: flatcal0 # A MKIDFlatdata or name of the same
+  wcscal: wcscal0 # A MKIDWCSCal or name of the same
+  speccal: '' # A MKIDSpecdata or name of the same
+  use: [] # Specify which dither obs to use, list or range specification string e.g. #,#-#,#,#
+  header: # A dictionary of fits header key overrides, to be applied to the observations
+    OBJECT: HIP 109427  # Object