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Kimberly Isobel Meechan
platy-browser-data
Commits
4bc50d05
Commit
4bc50d05
authored
5 years ago
by
Constantin Pape
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Add chromatin segmentation to data
parent
28f13eb2
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Changes
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3 changed files
data/rawdata/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
+39
-0
39 additions, 0 deletions
.../rawdata/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
make_initial_version.py
+15
-2
15 additions, 2 deletions
make_initial_version.py
update_platy_browser.py
+12
-3
12 additions, 3 deletions
update_platy_browser.py
with
66 additions
and
5 deletions
data/rawdata/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
0 → 100755
+
39
−
0
View file @
4bc50d05
<SpimData
version=
"0.2"
>
<BasePath
type=
"relative"
>
.
</BasePath>
<SequenceDescription>
<ImageLoader
format=
"bdv.hdf5"
>
<hdf5
type=
"relative"
>
sbem-6dpf-1-whole-segmented-chromatin-labels.h5
</hdf5>
</ImageLoader>
<ViewSetups>
<Attributes
name=
"channel"
>
<Channel>
<id>
1
</id>
<name>
1
</name>
</Channel>
</Attributes>
<ViewSetup>
<id>
0
</id>
<name>
channel 1
</name>
<size>
13750 12958 11416
</size>
<voxelSize>
<unit>
micrometer
</unit>
<size>
0.02 0.02 0.025
</size>
</voxelSize>
<attributes>
<channel>
1
</channel>
</attributes>
</ViewSetup>
</ViewSetups>
<Timepoints
type=
"range"
>
<first>
0
</first>
<last>
0
</last>
</Timepoints>
</SequenceDescription>
<ViewRegistrations>
<ViewRegistration
setup=
"0"
timepoint=
"0"
>
<ViewTransform
type=
"affine"
>
<affine>
0.02 0.0 0.0 0.0 0.0 0.02 0.0 0.0 0.0 0.0 0.025 0.0
</affine>
</ViewTransform>
</ViewRegistration>
</ViewRegistrations>
</SpimData>
This diff is collapsed.
Click to expand it.
make_initial_version.py
+
15
−
2
View file @
4bc50d05
...
...
@@ -8,6 +8,7 @@ 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.files
import
copy_segmentation
from
scripts.attributes
import
make_nucleus_tables
,
make_cell_tables
from
pybdv.converter
import
make_bdv
...
...
@@ -71,6 +72,18 @@ def make_prospr_region_segmentations():
unit
=
'
micrometer
'
,
resolution
=
[
0.5
,
0.5
,
0.5
])
def
insert_chromatin
():
src_folder
=
'
data/rawdata
'
dst_folder
=
'
data/0.2.0
'
name
=
'
sbem-6dpf-1-whole-segmented-chromatin-labels
'
copy_segmentation
(
src_folder
,
dst_folder
,
name
)
src_table
=
'
/g/arendt/EM_6dpf_segmentation/EM-Prospr/tables/em-segmented-chromatin-labels.csv
'
dst_table
=
os
.
path
.
join
(
dst_folder
,
'
tables
'
,
name
)
os
.
makedirs
(
dst_table
,
exist_ok
=
True
)
dst_table
=
os
.
path
.
join
(
dst_table
,
'
base.csv
'
)
copyfile
(
src_table
,
dst_table
)
def
make_initial_version
():
src_folder
=
'
data/rawdata
'
...
...
@@ -96,7 +109,7 @@ def make_initial_version():
os
.
path
.
join
(
folder
,
'
misc
'
,
'
bdvserver.txt
'
))
if
__name__
==
'
__main__
'
:
insert_chromatin
()
# make_prospr_region_segmentations()
make_initial_version
()
#
make_initial_version()
This diff is collapsed.
Click to expand it.
update_platy_browser.py
+
12
−
3
View file @
4bc50d05
...
...
@@ -102,8 +102,11 @@ def export_segmentations(folder, new_folder,
copy_segmentation
(
folder
,
new_folder
,
NAME_CILIA
)
# copy static segmentations
# we also treat the chromatin segmentation as static for now,
# but might change this at some point
static_seg_names
=
(
'
sbem-6dpf-1-whole-segmented-muscles
'
,
'
sbem-6dpf-1-whole-segmented-tissue-labels
'
)
'
sbem-6dpf-1-whole-segmented-tissue-labels
'
,
'
sbem-6dpf-1-whole-segmented-chromatin-labels
'
)
for
seg_name
in
static_seg_names
:
copy_segmentation
(
folder
,
new_folder
,
seg_name
)
...
...
@@ -134,7 +137,8 @@ def make_attributes(folder, new_folder,
copy_tables
(
folder
,
new_folder
,
NAME_CILIA
)
# copy tables associated with static segmentations
static_seg_names
=
(
'
sbem-6dpf-1-whole-segmented-tissue-labels
'
,)
static_seg_names
=
(
'
sbem-6dpf-1-whole-segmented-tissue-labels
'
,
'
sbem-6dpf-1-whole-segmented-chromatin-labels
'
)
for
seg_name
in
static_seg_names
:
copy_tables
(
folder
,
new_folder
,
seg_name
)
...
...
@@ -198,7 +202,10 @@ def update_platy_browser(update_cell_segmentation=False,
update_cell_tables
,
update_nucleus_tables
,
update_cilia_tables
)
if
not
update_dict
[
'
have_changes
'
]:
# if an explicit tag was given, we force an update
force_update
=
new_tag
!=
''
if
not
update_dict
[
'
have_changes
'
]
and
not
force_update
:
print
(
"
Nothing needs to be update, skipping
"
)
return
...
...
@@ -240,6 +247,8 @@ def update_platy_browser(update_cell_segmentation=False,
update_cilia_tables
,
target
=
target
,
max_jobs
=
max_jobs
)
# TODO add some quality control that cheks that all files are there
# TODO implement make release properly
return
# make new release
...
...
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