From 88b0672fa8f3531c3f8b471e858336eb51a20ecb Mon Sep 17 00:00:00 2001
From: arother <rother@neuro.mpg.de>
Date: Tue, 25 Apr 2023 17:22:16 +0200
Subject: [PATCH] updated str2int, int2str_converter with glia cell classes
---
syconn/extraction/cs_processing_steps.py | 14 ++++++++++++++
syconn/handler/prediction.py | 9 +++++++++
2 files changed, 23 insertions(+)
diff --git a/syconn/extraction/cs_processing_steps.py b/syconn/extraction/cs_processing_steps.py
index 6108f789..0f202f01 100755
--- a/syconn/extraction/cs_processing_steps.py
+++ b/syconn/extraction/cs_processing_steps.py
@@ -1338,17 +1338,23 @@ def create_syn_rfc(sd_syn_ssv: 'segmentation.SegmentationDataset', path2file: st
df = pandas.read_excel(path2file, header=0, names=[
'ixs', 'coord', 'pre', 'post', 'syn', 'doublechecked', 'triplechecked', '?', 'comments']).values
df = df[:, :7]
+ synaptic = 0
+ non_synaptic = 0
for ix in range(df.shape[0]):
c_orig = df[ix, 5]
c = df[ix, 6]
if type(c) != float and 'yes' in c:
unified_comment = 'synaptic'
+ synaptic += 1
elif type(c) != float and 'no' in c:
unified_comment = 'non-synaptic'
+ non_synaptic += 1
elif 'yes' in c_orig:
unified_comment = 'synaptic'
+ synaptic += 1
elif 'no' in c_orig:
unified_comment = 'non-synaptic'
+ non_synaptic += 1
else:
log.warn(f'Did not understand GT comment "{c}". Skipping')
continue
@@ -1357,6 +1363,7 @@ def create_syn_rfc(sd_syn_ssv: 'segmentation.SegmentationDataset', path2file: st
labels = np.array(labels)
label_coords = np.array(label_coords)
+ log.info(f'Before filtering: {synaptic} synaptic labels and {non_synaptic} non_synaptic labels')
# get deterministic order by sorting by coordinate first and then seeded shuffling
ixs = [i[0] for i in sorted(enumerate(label_coords),
@@ -1389,8 +1396,15 @@ def create_syn_rfc(sd_syn_ssv: 'segmentation.SegmentationDataset', path2file: st
if np.sum(mask) == 0:
raise ValueError
synssv_ids = synssv_ids[mask]
+ not_mapped_labels = labels[mask == 0]
+ not_mapped_syn = not_mapped_labels[not_mapped_labels == 'synaptic']
+ not_mapped_nonsyn = not_mapped_labels[not_mapped_labels == 'non-synaptic']
labels = labels[mask]
+ mapped_syn = labels[labels == 'synaptic']
+ mapped_nonsyn = labels[labels == 'non-synaptic']
log.info(f'Found {np.sum(mask)}/{len(mask)} samples with a distance < {max_dist_vx} vx to the target.')
+ log.info(f'Excluding {len(not_mapped_syn)} synaptic labels and {len(not_mapped_nonsyn)} non_synaptic labels after filtering')
+ log.info(f'Training with {len(mapped_syn)} synaptic labels and {len(mapped_nonsyn)} non_synaptic labels after filtering')
log.info(f'Synapse features will now be generated.')
features = []
diff --git a/syconn/handler/prediction.py b/syconn/handler/prediction.py
index caaf35b8..761081e4 100755
--- a/syconn/handler/prediction.py
+++ b/syconn/handler/prediction.py
@@ -1324,6 +1324,10 @@ def str2int_converter(comment: str, gt_type: str) -> int:
str2int_label = dict(STN=0, DA=1, MSN=2, LMAN=3, HVC=4, TAN=5, GPe=6, GPi=7,
FS=8, LTS=9, NGF=10)
return str2int_label[comment]
+ elif gt_type == 'ctgt_j0251_v3':
+ str2int_label = dict(STN=0, DA=1, MSN=2, LMAN=3, HVC=4, TAN=5, GPe=6, GPi=7,
+ FS=8, LTS=9, NGF=10, ASTRO=11, OLIGO=12, MICRO=13, FRAG=14)
+ return str2int_label[comment]
else:
raise ValueError("Given groundtruth type is not valid.")
@@ -1400,5 +1404,10 @@ def int2str_converter(label: int, gt_type: str) -> str:
FS=8, LTS=9, NGF=10)
int2str_label = {v: k for k, v in str2int_label.items()}
return int2str_label[label]
+ elif gt_type == 'ctgt_j0251_v3':
+ str2int_label = dict(STN=0, DA=1, MSN=2, LMAN=3, HVC=4, TAN=5, GPe=6, GPi=7,
+ FS=8, LTS=9, NGF=10, ASTRO=11, OLIGO=12, MICRO=13, FRAG=14)
+ int2str_label = {v: k for k, v in str2int_label.items()}
+ return int2str_label[label]
else:
raise ValueError("Given ground truth type is not valid.")
--
GitLab