Reply to reviewer comments.

Add TOTFlux explicitly.

Hook up TOTFlux output.

Fix linting.

data/ppdb-ap-pipe-schema-extra.yaml

@@ -17,7 +17,114 @@ columns:
   type: INT
   nullable: false
   description: Total number of DiaSources associated with this DiaObject.
-
+- name: uTOTFluxMean
+  type: FLOAT
+  nullable: true
+  description: Weighted mean forced photometry flux for u filter.
+  ucd: phot.count
+  unit: nJy
+- name: uTOTFluxMeanErr
+  type: FLOAT
+  nullable: true
+  description: Standard error of uTOTFluxMean.
+  ucd: stat.error
+  unit: nJy
+- name: uTOTFluxSigma
+  type: FLOAT
+  nullable: true
+  description: Standard deviation of the distribution of uTOTFlux.
+  ucd: stat.stdev
+  unit: nJy
+- name: gTOTFluxMean
+  type: FLOAT
+  nullable: true
+  description: Weighted mean forced photometry flux for g filter.
+  ucd: phot.count
+  unit: nJy
+- name: gTOTFluxMeanErr
+  type: FLOAT
+  nullable: true
+  description: Standard error of gTOTFluxMean.
+  ucd: stat.error
+  unit: nJy
+- name: gTOTFluxSigma
+  type: FLOAT
+  nullable: true
+  description: Standard deviation of the distribution of gTOTFlux.
+  ucd: stat.stdev
+  unit: nJy
+- name: rTOTFluxMean
+  type: FLOAT
+  nullable: true
+  description: Weighted mean forced photometry flux for r filter.
+  ucd: phot.count
+  unit: nJy
+- name: rTOTFluxMeanErr
+  type: FLOAT
+  nullable: true
+  description: Standard error of rTOTFluxMean.
+  ucd: stat.error
+  unit: nJy
+- name: rTOTFluxSigma
+  type: FLOAT
+  nullable: true
+  description: Standard deviation of the distribution of rTOTFlux.
+  ucd: stat.stdev
+  unit: nJy
+- name: iTOTFluxMean
+  type: FLOAT
+  nullable: true
+  description: Weighted mean forced photometry flux for i filter.
+  ucd: phot.count
+  unit: nJy
+- name: iTOTFluxMeanErr
+  type: FLOAT
+  nullable: true
+  description: Standard error of iTOTFluxMean.
+  ucd: stat.error
+  unit: nJy
+- name: iTOTFluxSigma
+  type: FLOAT
+  nullable: true
+  description: Standard deviation of the distribution of iTOTFlux.
+  ucd: stat.stdev
+  unit: nJy
+- name: zTOTFluxMean
+  type: FLOAT
+  nullable: true
+  description: Weighted mean forced photometry flux for z filter.
+  ucd: phot.count
+  unit: nJy
+- name: zTOTFluxMeanErr
+  type: FLOAT
+  nullable: true
+  description: Standard error of zTOTFluxMean.
+  ucd: stat.error
+  unit: nJy
+- name: zTOTFluxSigma
+  type: FLOAT
+  nullable: true
+  description: Standard deviation of the distribution of zTOTFlux.
+  ucd: stat.stdev
+  unit: nJy
+- name: yTOTFluxMean
+  type: FLOAT
+  nullable: true
+  description: Weighted mean forced photometry flux for y filter.
+  ucd: phot.count
+  unit: nJy
+- name: yTOTFluxMeanErr
+  type: FLOAT
+  nullable: true
+  description: Standard error of yTOTFluxMean.
+  ucd: stat.error
+  unit: nJy
+- name: yTOTFluxSigma
+  type: FLOAT
+  nullable: true
+  description: Standard deviation of the distribution of yTOTFlux.
+  ucd: stat.stdev
+  unit: nJy
 - name: uPSFluxMedian
   type: FLOAT
   nullable: true
@@ -70,7 +177,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Linear best fit slope of the u band fluxes.
-  unit: nJy/MJD
+  unit: nJy/day
 - name: uPSFluxLinearIntercept
   type: FLOAT
   nullable: true
@@ -79,7 +186,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Maximum slope between u band flux obsevations max(delta_flux/delta_time)
-  unit: nJy/MJD
+  unit: nJy/day
 - name: uPSFluxErrMean
   type: FLOAT
   nullable: true
@@ -138,7 +245,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Linear best fit slope of the g band fluxes.
-  unit: nJy/MJD
+  unit: nJy/day
 - name: gPSFluxLinearIntercept
   type: FLOAT
   nullable: true
@@ -148,7 +255,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Maximum slope between g band flux obsevations max(delta_flux/delta_time)
-  unit: nJy/MJD
+  unit: nJy/day
 - name: gPSFluxErrMean
   type: FLOAT
   nullable: true
@@ -207,7 +314,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Linear best fit slope of the r band fluxes.
-  unit: nJy/MJD
+  unit: nJy/day
 - name: rPSFluxLinearIntercept
   type: FLOAT
   nullable: true
@@ -217,7 +324,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Maximum slope between r band flux obsevations max(delta_flux/delta_time)
-  unit: nJy/MJD
+  unit: nJy/day
 - name: rPSFluxErrMean
   type: FLOAT
   nullable: true
@@ -276,7 +383,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Linear best fit slope of the i band fluxes.
-  unit: nJy/MJD
+  unit: nJy/day
 - name: iPSFluxLinearIntercept
   type: FLOAT
   nullable: true
@@ -286,7 +393,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Maximum slope between i band flux obsevations max(delta_flux/delta_time)
-  unit: nJy/MJD
+  unit: nJy/day
 - name: iPSFluxErrMean
   type: FLOAT
   nullable: true
@@ -345,7 +452,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Linear best fit slope of the z band fluxes.
-  unit: nJy/MJD
+  unit: nJy/day
 - name: zPSFluxLinearIntercept
   type: FLOAT
   nullable: true
@@ -355,7 +462,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Maximum slope between z band flux obsevations max(delta_flux/delta_time)
-  unit: nJy/MJD
+  unit: nJy/day
 - name: zPSFluxErrMean
   type: FLOAT
   nullable: true
@@ -414,7 +521,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Linear best fit slope of the y band fluxes.
-  unit: nJy/MJD
+  unit: nJy/day
 - name: yPSFluxLinearIntercept
   type: FLOAT
   nullable: true
@@ -424,7 +531,7 @@ columns:
   type: FLOAT
   nullable: true
   description: Maximum slope between y band flux obsevations max(delta_flux/delta_time)
-  unit: nJy/MJD
+  unit: nJy/day
 - name: yPSFluxErrMean
   type: FLOAT
   nullable: true

python/lsst/ap/association/afwUtils.py

@@ -104,7 +104,6 @@ def make_dia_object_schema(filter_names=None):
                     doc='Standard error of uPSFluxMean.')
     schema.addField('uPSFluxSigma', type='F',
                     doc='Standard deviation of the distribution of uPSFlux.')
-
     schema.addField('uPSFluxChi2', type='F',
                     doc='Chi^2 statistic for the scatter of uPSFlux around uPSFluxMean.')
     schema.addField('uPSFluxNdata', type='I',
@@ -121,7 +120,6 @@ def make_dia_object_schema(filter_names=None):
                     doc='Standard error of gPSFluxMean.')
     schema.addField('gPSFluxSigma', type='F',
                     doc='Standard deviation of the distribution of gPSFlux.')
-
     schema.addField('gPSFluxChi2', type='F',
                     doc='Chi^2 statistic for the scatter of gPSFlux around gPSFluxMean.')
     schema.addField('gPSFluxNdata', type='I',
@@ -263,7 +261,42 @@ def make_dia_object_schema(filter_names=None):
                     doc='Last time when non-forced DIASource was seen for this object')
     schema.addField('nDiaSources', type='I',
                     doc='Total number of DiaSources associated with this DiaObject.')
-
+    schema.addField('uTOTFluxMean', type='F',
+                    doc='Weighted mean forced photometry flux for u filter.')
+    schema.addField('uTOTFluxMeanErr', type='F',
+                    doc='Standard error of uTOTFluxMean.')
+    schema.addField('uTOTFluxSigma', type='F',
+                    doc='Standard deviation of the distribution of uTOTFlux.')
+    schema.addField('gTOTFluxMean', type='F',
+                    doc='Weighted mean forced photometry flux for g filter.')
+    schema.addField('gTOTFluxMeanErr', type='F',
+                    doc='Standard error of uTOTFluxMean.')
+    schema.addField('gTOTFluxSigma', type='F',
+                    doc='Standard deviation of the distribution of gTOTFlux.')
+    schema.addField('rTOTFluxMean', type='F',
+                    doc='Weighted mean forced photometry flux for r filter.')
+    schema.addField('rTOTFluxMeanErr', type='F',
+                    doc='Standard error of uTOTFluxMean.')
+    schema.addField('rTOTFluxSigma', type='F',
+                    doc='Standard deviation of the distribution of rTOTFlux.')
+    schema.addField('iTOTFluxMean', type='F',
+                    doc='Weighted mean forced photometry flux for i filter.')
+    schema.addField('iTOTFluxMeanErr', type='F',
+                    doc='Standard error of uTOTFluxMean.')
+    schema.addField('iTOTFluxSigma', type='F',
+                    doc='Standard deviation of the distribution of iTOTFlux.')
+    schema.addField('zTOTFluxMean', type='F',
+                    doc='Weighted mean forced photometry flux for z filter.')
+    schema.addField('zTOTFluxMeanErr', type='F',
+                    doc='Standard error of uTOTFluxMean.')
+    schema.addField('zTOTFluxSigma', type='F',
+                    doc='Standard deviation of the distribution of zTOTFlux.')
+    schema.addField('yTOTFluxMean', type='F',
+                    doc='Weighted mean forced photometry flux for y filter.')
+    schema.addField('yTOTFluxMeanErr', type='F',
+                    doc='Standard error of uTOTFluxMean.')
+    schema.addField('yTOTFluxSigma', type='F',
+                    doc='Standard deviation of the distribution of yTOTFlux.')
     schema.addField('uPSFluxMedian', type='F',
                     doc='Median u band flux.')
     schema.addField('uPSFluxMAD', type='F',

python/lsst/ap/association/association.py

@@ -129,7 +129,7 @@ def _set_flux_stats(dia_object_record, dia_sources, filter_name, filter_id):
         dia_object_record['%sPSFluxLinearSlope' % filter_name] = m
         dia_object_record['%sPSFluxLinearIntercept' % filter_name] = b
 
-        dia_object_record['%sPSFluxStetsonJ' % filter_name] = _stentson_J(
+        dia_object_record['%sPSFluxStetsonJ' % filter_name] = _stetson_J(
             fluxes, fluxErrors)
 
         dia_object_record['%sPSFluxErrMean' % filter_name] = \
@@ -143,14 +143,14 @@ def _set_flux_stats(dia_object_record, dia_sources, filter_name, filter_id):
     totFluxErrors = totFluxErrors[noNanMask]
 
     if len(totFluxes) == 1:
-        dia_object_record['%sFPFluxMean' % filter_name] = totFluxes
+        dia_object_record['%sTOTFluxMean' % filter_name] = totFluxes
     elif len(totFluxes) > 1:
         fluxMean = np.average(totFluxes, weights=1 / totFluxErrors ** 2)
-        dia_object_record['%sFPFluxMean' % filter_name] = fluxMean
-        dia_object_record['%sFPFluxMeanErr' % filter_name] = np.sqrt(
+        dia_object_record['%sTOTFluxMean' % filter_name] = fluxMean
+        dia_object_record['%sTOTFluxMeanErr' % filter_name] = np.sqrt(
             1 / np.sum(1 / totFluxErrors ** 2))
-        dia_object_record['%sFPFluxSigma' % filter_name] = np.std(totFluxes,
-                                                                  ddof=1)
+        dia_object_record['%sTOTFluxSigma' % filter_name] = np.std(totFluxes,
+                                                                   ddof=1)
 
 
 def _fit_linear_flux_model(fluxes, errors, times):
@@ -177,8 +177,8 @@ def model(x):
     return ans
 
 
-def _stentson_J(fluxes, errors):
-    """Compute the single band StentsonJ statistic.
+def _stetson_J(fluxes, errors):
+    """Compute the single band stetsonJ statistic.
 
     Parameters
     ----------
@@ -189,23 +189,28 @@ def _stentson_J(fluxes, errors):
 
     Returns
     -------
-    stentsonJ : `float`
-        StentsonJ statistic for the input fluxes and errors.
+    stetsonJ : `float`
+        stetsonJ statistic for the input fluxes and errors.
+
+    References
+    ----------
+    .. [1] Stetson, P. B., "On the Automatic Determination of Light-Curve
+       Parameters for Cepheid Variables", PASP, 108, 851S, 1996
     """
     n_points = len(fluxes)
-    flux_mean = _stentson_mean(fluxes, errors)
+    flux_mean = _stetson_mean(fluxes, errors)
     delta_val = (
         np.sqrt(n_points / (n_points - 1)) * (fluxes - flux_mean) / errors)
     p_k = delta_val ** 2 - 1
 
     return np.mean(np.sign(p_k) * np.sqrt(np.fabs(p_k)))
 
 
-def _stentson_mean(values, errors, alpha=2., beta=2., n_iter=20, tol=1e-6):
-    """Compute the Stentson mean of the fluxes which down-weights outliers.
+def _stetson_mean(values, errors, alpha=2., beta=2., n_iter=20, tol=1e-6):
+    """Compute the stetson mean of the fluxes which down-weights outliers.
 
     Weighted biased on an error weighted difference scaled by a constant
-    (1/``a``) and raised to the power beta. Higher beta's more harshly penalize
+    (1/``a``) and raised to the power beta. Higher betas more harshly penalize
     outliers and ``a`` sets the number of sigma where a weighted difference of
     1 occurs.
 
@@ -229,7 +234,12 @@ def _stentson_mean(values, errors, alpha=2., beta=2., n_iter=20, tol=1e-6):
     Returns
     -------
     wmean : `float`
-        Weighted Stentson mean result.
+        Weighted stetson mean result.
+
+    References
+    ----------
+    .. [1] Stetson, P. B., "On the Automatic Determination of Light-Curve
+       Parameters for Cepheid Variables", PASP, 108, 851S, 1996
     """
     n_points = len(values)
     n_factor = np.sqrt(n_points / (n_points - 1))