From a082f5b64a68d0dbd5ce0c32643ffb48ba744136 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Mon, 8 Jul 2019 14:33:56 +0200
Subject: [PATCH] Update prospr segmented regions
---
...-6dpf-1-whole-segmented-CrypticSegment.xml | 12 +++++-----
.../prospr-6dpf-1-whole-segmented-Head.xml | 12 +++++-----
.../prospr-6dpf-1-whole-segmented-PNS.xml | 12 +++++-----
...prospr-6dpf-1-whole-segmented-Pygidium.xml | 12 +++++-----
...pr-6dpf-1-whole-segmented-RestOfAnimal.xml | 12 +++++-----
...rospr-6dpf-1-whole-segmented-Stomodeum.xml | 12 +++++-----
.../prospr-6dpf-1-whole-segmented-VNC.xml | 12 +++++-----
make_initial_version.py | 22 +++++++++++++++++++
8 files changed, 64 insertions(+), 42 deletions(-)
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-CrypticSegment.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-CrypticSegment.xml
index 4272f85..c756b3c 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-CrypticSegment.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-CrypticSegment.xml
@@ -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>
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-Head.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-Head.xml
index 1d624ec..de6c251 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-Head.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-Head.xml
@@ -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>
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-PNS.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-PNS.xml
index 2e3f4c9..fd9e36f 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-PNS.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-PNS.xml
@@ -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>
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-Pygidium.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-Pygidium.xml
index d2d0ccb..b9b4060 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-Pygidium.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-Pygidium.xml
@@ -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>
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml
index ff71c06..d97dd9d 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml
@@ -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>
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-Stomodeum.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-Stomodeum.xml
index 9439922..7f409ff 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-Stomodeum.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-Stomodeum.xml
@@ -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>
diff --git a/data/rawdata/prospr-6dpf-1-whole-segmented-VNC.xml b/data/rawdata/prospr-6dpf-1-whole-segmented-VNC.xml
index 5072ebd..77ea228 100644
--- a/data/rawdata/prospr-6dpf-1-whole-segmented-VNC.xml
+++ b/data/rawdata/prospr-6dpf-1-whole-segmented-VNC.xml
@@ -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>
diff --git a/make_initial_version.py b/make_initial_version.py
index aa993ae..f8528b2 100755
--- a/make_initial_version.py
+++ b/make_initial_version.py
@@ -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()
--
GitLab