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support class scores CSVs #102

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support class scores CSVs #102

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25 changes: 25 additions & 0 deletions ifcb/data/products/class_scores.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,13 +49,21 @@ def _get_v3_file(self, bin_lid):
if path is not None:
return ClassScoresFile(path, bin_lid, version=3)
raise KeyError(bin_lid)
def _get_v4_file(self, bin_lid):
filename = '{}.csv'.format(bin_lid)
path = find_product_file(self.path, filename, exhaustive=self.exhaustive)
if path is not None:
return ClassScoresFile(path, bin_lid, version=4)
raise KeyError(bin_lid)
def __getitem__(self, bin_lid):
if self.version == 1:
return self._get_v1_file(bin_lid)
elif self.version == 2:
return self._get_v2_file(bin_lid)
elif self.version == 3:
return self._get_v3_file(bin_lid)
elif self.version == 4:
return self._get_v4_file(bin_lid)
else:
raise KeyError('unknown class scores version {}'.format(self.version))
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def has_key(self, bin_lid):
Expand All @@ -71,6 +79,10 @@ def keys(self):
fn_regex = r'.*_class_v2\.h5'
elif self.version == 3:
fn_regex = r'.*_class.h5'
elif self.version == 4:
fn_regex = r'.*\.csv'
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else:
raise KeyError('unknown class scores version {}'.format(self.version))
for p in list_product_files(self.path, fn_regex):
# parse the filename as a pid
bin_lid = Pid(os.path.basename(p)).bin_lid
Expand Down Expand Up @@ -108,12 +120,25 @@ def _class_scores_v3(self):
class_labels = [l.decode('ascii') for l in f['class_labels'][:]]
roi_numbers = f['roi_numbers'][:]
return self._cs2df(scores, class_labels, roi_numbers)
def _class_scores_v4(self):
# version 4 is a CSV file, the first column is "pid" which is a string that contains the ROI number
df = pd.read_csv(self.path, index_col='pid')
# the index is the pid, which contains the roi number
df.index = df.index.str.extract(r'_(\d+)$')[0]
df.index.name = 'roi_number'
# convert index to int
roi_numbers = df.index.astype(int)
class_labels = df.columns.tolist()
scores = df.values
return self._cs2df(scores, class_labels, roi_numbers)
def class_scores(self):
if self.version == 1:
return self._class_scores_v1()
elif self.version == 2:
return self._class_scores_v2()
elif self.version == 3:
return self._class_scores_v3()
elif self.version == 4:
return self._class_scores_v4()
else:
raise KeyError('unknown class scores version {}'.format(self.version))