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Commit a082f5b6 authored by Constantin Pape's avatar Constantin Pape
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Update prospr segmented regions

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1 merge request!2Merge versioning and scripts into master
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data/rawdata/prospr-6dpf-1-whole-segmented-CrypticSegment.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-CrypticSegment.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
data/rawdata/prospr-6dpf-1-whole-segmented-Head.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-Head.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
data/rawdata/prospr-6dpf-1-whole-segmented-PNS.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-PNS.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
data/rawdata/prospr-6dpf-1-whole-segmented-Pygidium.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-Pygidium.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
data/rawdata/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-RestOfAnimal.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
data/rawdata/prospr-6dpf-1-whole-segmented-Stomodeum.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-Stomodeum.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
data/rawdata/prospr-6dpf-1-whole-segmented-VNC.xml
+ 6
− 6
View file @ a082f5b6
......@@ -5,6 +5,12 @@
<hdf5 type="relative">prospr-6dpf-1-whole-segmented-VNC.h5</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
<ViewSetup>
<id>0</id>
<name>channel 1</name>
......@@ -17,12 +23,6 @@
<channel>1</channel>
</attributes>
</ViewSetup>
<Attributes name="channel">
<Channel>
<id>1</id>
<name>1</name>
</Channel>
</Attributes>
</ViewSetups>
<Timepoints type="range">
<first>0</first>
......
make_initial_version.py
+ 22
− 0
View file @ a082f5b6
......@@ -2,11 +2,14 @@
import os
from shutil import copyfile
from glob import glob
import h5py
from scripts.files import make_folder_structure
from scripts.export import export_segmentation
from scripts.files import make_bdv_server_file, copy_image_data, copy_misc_data
from scripts.attributes import make_nucleus_tables, make_cell_tables
from pybdv.converter import make_bdv
def make_sbem_segmentations(old_folder, folder):
......@@ -51,6 +54,23 @@ def make_sbem_tables(folder):
copyfile(tissue_table_in, tissue_table_out)
def make_prospr_region_segmentations():
in_prefix = '/g/arendt/EM_6dpf_segmentation/EM-Prospr/BodyPart_*.h5'
out_prefix = './data/rawdata/prospr-6dpf-1-whole-segmented-'
files = glob(in_prefix)
for p in files:
name = p.split('_')[-1][:-3]
o = out_prefix + name + '.h5'
print(p, "to", o)
with h5py.File(p) as f:
key = 't00000/s00/0/cells'
data = f[key][:]
data[data > 0] = 0
data[data < 0] = 255
make_bdv(data, o, 3 * [[2, 2, 2]],
unit='micrometer', resolution=[0.5, 0.5, 0.5])
def make_initial_version():
src_folder = 'data/rawdata'
......@@ -76,5 +96,7 @@ def make_initial_version():
os.path.join(folder, 'misc', 'bdvserver.txt'))
if __name__ == '__main__':
# make_prospr_region_segmentations()
make_initial_version()
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