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accessing default features keys #223

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accessing default features keys #223

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13 changes: 7 additions & 6 deletions lazyflow/operators/ioOperators/opExportToKnime.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import vigra
import numpy
import math
from ilastik.applets.objectExtraction.opObjectExtraction import default_features_key

def write_numpy_structured_array_to_HDF5(fid, internalPath, data, overwrite = False):
"""
Expand Down Expand Up @@ -175,10 +176,10 @@ def write_to_h5(self, table, image_paths, roi):
raw_shape = self.RawImage.meta.getTaggedShape()
nchannels = raw_shape['c']
try:
minxs = table["Default features, Coord<Minimum>_ch_0"].astype(numpy.int32)
minys = table["Default features, Coord<Minimum>_ch_1"].astype(numpy.int32)
maxxs = table["Default features, Coord<Maximum>_ch_0"].astype(numpy.int32)
maxys = table["Default features, Coord<Maximum>_ch_1"].astype(numpy.int32)
minxs = table[default_features_key+", Coord<Minimum>_ch_0"].astype(numpy.int32)
minys = table[default_features_key+", Coord<Minimum>_ch_1"].astype(numpy.int32)
maxxs = table[default_features_key+", Coord<Maximum>_ch_0"].astype(numpy.int32)
maxys = table[default_features_key+", Coord<Maximum>_ch_1"].astype(numpy.int32)
time_values = table["Time"].astype(numpy.int32)
except ValueError:
logger.info("Object bounding boxes are not passed as features. Object images will not be saved")
Expand All @@ -187,8 +188,8 @@ def write_to_h5(self, table, image_paths, roi):
image_paths["labels"][i] = ""
else:
try:
minzs = table["Default features, Coord<Minimum>_ch_2"].astype(numpy.int32)
maxzs = table["Default features, Coord<Maximum>_ch_2"].astype(numpy.int32)
minzs = table[default_features_key+", Coord<Minimum>_ch_2"].astype(numpy.int32)
maxzs = table[default_features_key+", Coord<Maximum>_ch_2"].astype(numpy.int32)
except ValueError:
minzs = None
maxzs = None
Expand Down