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DM-16518 Write footprints table for Firefly viewer in binary2 format #22

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merged 3 commits into from
Nov 29, 2018
Merged

DM-16518 Write footprints table for Firefly viewer in binary2 format #22

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ad9afb3
add conversions to make binary2 work
stargaser Nov 15, 2018
81b371c
work with astropy table until end
stargaser Nov 27, 2018
790031e
use slot_Centroids first for footprint centers
stargaser Nov 27, 2018
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93 changes: 37 additions & 56 deletions python/lsst/display/firefly/footprints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,11 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.

from copy import deepcopy

import numpy as np
from astropy.io.votable.tree import VOTableFile, Resource, Field, Info
from astropy.io.votable.tree import Info
from astropy.io.votable import from_table
import astropy.units as u
from astropy.table import Column

import lsst.afw.geom as afwGeom
import lsst.afw.table as afwTable
Expand Down Expand Up @@ -85,49 +84,12 @@ def createFootprintsTable(catalog, xy0=None, insertColumn=4):
_catalog.extend(catalog, deep=True)
sourceTable = _catalog.asAstropy()

# Fix invalid unit strings of "seconds"
# Ticket DM-16411 has been filed to fix this upstream
for colName in ['modelfit_CModel_dev_time', 'modelfit_CModel_initial_time',
'modelfit_CModel_exp_time']:
if colName in sourceTable.colnames:
sourceTable[colName].unit = u.s

# Change int64 dtypes so they convert to VOTable
for colName in sourceTable.colnames:
if sourceTable[colName].dtype.num == 9:
sourceTable[colName].dtype = np.dtype('long')

# Convert the astropy.table.Table to astropy.vo.voTableFile
inputVoFile = from_table(sourceTable)
# Extract first (only) table
inputVoTable = inputVoFile.get_first_table()
# delete the Astropy table after saving the columns
inputColumnNames = sourceTable.colnames
del sourceTable
# Make a copy of the table, because adding columns will cause the data
# to be destroyed, and we will have to copy the data back from the input
outTable = deepcopy(inputVoTable)

voTableFile = VOTableFile()
resource = Resource()
voTableFile.resources.append(resource)
resource.tables.append(outTable)
outTable.fields.insert(insertColumn, Field(voTableFile, name='family_id',
datatype='long', arraysize='1'))
outTable.fields.insert(insertColumn+1, Field(voTableFile, name='category',
datatype='unicodeChar', arraysize='*'))
outTable.fields.extend([
Field(voTableFile, name="spans", datatype="int", arraysize="*"),
Field(voTableFile, name="peaks", datatype="float", arraysize="*"),
Field(voTableFile, name='footprint_corner1_x', datatype="int", arraysize="1"),
Field(voTableFile, name='footprint_corner1_y', datatype="int", arraysize="1"),
Field(voTableFile, name='footprint_corner2_x', datatype="int", arraysize="1"),
Field(voTableFile, name='footprint_corner2_y', datatype="int", arraysize="1")])

nRows = len(inputVoTable.array)

# This next step destroys the existing data
outTable.create_arrays(nrows=nRows)

x0, y0 = xy0
spanList = []
Expand All @@ -143,6 +105,9 @@ def createFootprintsTable(catalog, xy0=None, insertColumn=4):
recordId = record.getId()
spans = footprint.getSpans()
scoords = [(s.getY()-y0, s.getX0()-x0, s.getX1()-x0) for s in spans]
scoords = np.array(scoords).flatten()
scoords = np.ma.MaskedArray(scoords, mask=np.zeros(len(scoords),
dtype=np.bool))
fpbbox = footprint.getBBox()
corners = [(c.getX()-x0, c.getY()-y0) for c in fpbbox.getCorners()]
fpxll.append(corners[0][0])
Expand All @@ -151,6 +116,10 @@ def createFootprintsTable(catalog, xy0=None, insertColumn=4):
fpyur.append(corners[2][1])
peaks = footprint.getPeaks()
pcoords = [(p.getFx()-x0, p.getFy()-y0) for p in peaks]
pcoords = np.array(pcoords).flatten()
pcoords = np.ma.MaskedArray(pcoords, mask=np.zeros(len(pcoords),
dtype=np.bool))
fpbbox = footprint.getBBox()
parentId = record.getParent()
nChild = record.get('deblend_nChild')
if parentId == 0:
Expand All @@ -168,19 +137,21 @@ def createFootprintsTable(catalog, xy0=None, insertColumn=4):
spanList.append(scoords)
peakList.append(pcoords)

# Copy the input data to the output
for f in inputVoTable.fields:
outTable.array[f.name] = inputVoTable.array[f.name]
# The numerical columns need to be reshaped
outTable.array['family_id'] = np.ma.MaskedArray(familyList).reshape((nRows, 1))
# The object columns are not reshaped
outTable.array['category'] = np.ma.MaskedArray(categoryList)
outTable.array['spans'] = np.ma.MaskedArray(spanList)
outTable.array['peaks'] = np.ma.MaskedArray(peakList)
outTable.array['footprint_corner1_x'] = np.ma.MaskedArray(fpxll).reshape((nRows, 1))
outTable.array['footprint_corner1_y'] = np.ma.MaskedArray(fpyll).reshape((nRows, 1))
outTable.array['footprint_corner2_x'] = np.ma.MaskedArray(fpxur).reshape((nRows, 1))
outTable.array['footprint_corner2_y'] = np.ma.MaskedArray(fpyur).reshape((nRows, 1))
sourceTable.add_column(Column(np.array(familyList)),
name='family_id',
index=insertColumn)
sourceTable.add_column(Column(np.array(categoryList)),
name='category',
index=insertColumn+1)
sourceTable.add_column(Column(np.array(spanList)), name='spans')
sourceTable.add_column(Column(np.array(peakList)), name='peaks')
sourceTable.add_column(Column(np.array(fpxll)), name='footprint_corner1_x')
sourceTable.add_column(Column(np.array(fpyll)), name='footprint_corner1_y')
sourceTable.add_column(Column(np.array(fpxur)), name='footprint_corner2_x')
sourceTable.add_column(Column(np.array(fpyur)), name='footprint_corner2_y')

outputVO = from_table(sourceTable)
outTable = outputVO.get_first_table()

outTable.infos.append(Info(name='contains_lsst_footprints', value='true'))
outTable.infos.append(Info(name='contains_lsst_measurements', value='true'))
Expand All @@ -189,7 +160,12 @@ def createFootprintsTable(catalog, xy0=None, insertColumn=4):
'footprint_corner2_x;footprint_corner2_y;spans;peaks'))
outTable.infos.append(Info(name='pixelsys', value='zero-based'))
# Check whether the coordinates are included and are valid
if (('coord_ra' in inputColumnNames) and
if (('slot_Centroid_x' in inputColumnNames) and
('slot_Centroid_y' in inputColumnNames) and
np.isfinite(outTable.array['slot_Centroid_x']).any() and
np.isfinite(outTable.array['slot_Centroid_y']).any()):
coord_column_string = 'slot_Centroid_x;slot_Centroid_y;ZERO_BASED'
elif (('coord_ra' in inputColumnNames) and
('coord_dec' in inputColumnNames) and
np.isfinite(outTable.array['coord_ra']).any() and
np.isfinite(outTable.array['coord_dec']).any()):
Expand All @@ -209,6 +185,11 @@ def createFootprintsTable(catalog, xy0=None, insertColumn=4):
outTable.infos.append(Info(name='CatalogCoordColumns',
value=coord_column_string))

outTable.format = 'tabledata'
for f in outTable.fields:
if f.datatype == 'bit':
f.datatype = 'boolean'

outTable._config['version_1_3_or_later'] = True
outputVO.set_all_tables_format('binary2')

return(voTableFile)
return(outputVO)