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imcf
python-imcflibs
Commits
eabdfcf8
Commit
eabdfcf8
authored
6 years ago
by
Niko Ehrenfeuchter
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Re-activate logging in imagej.projections and imagej.shading
parent
ca29501b
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2 changed files
src/imcflibs/imagej/projections.py
+4
-3
4 additions, 3 deletions
src/imcflibs/imagej/projections.py
src/imcflibs/imagej/shading.py
+3
-1
3 additions, 1 deletion
src/imcflibs/imagej/shading.py
with
7 additions
and
4 deletions
src/imcflibs/imagej/projections.py
+
4
−
3
View file @
eabdfcf8
"""
Functions for creating Z projections.
"""
from
.bioformats
import
export_using_orig_name
from
..log
import
LOG
as
log
from
ij.plugin
import
ZProjector
...
...
@@ -18,7 +19,7 @@ def average(imp):
ij.ImagePlus
The result of the projection.
"""
#
log.debug("Creating average projection...")
log
.
debug
(
"
Creating average projection...
"
)
proj
=
ZProjector
.
run
(
imp
,
"
avg
"
)
return
proj
...
...
@@ -36,7 +37,7 @@ def maximum(imp):
ij.ImagePlus
The result of the projection.
"""
#
log.debug("Creating maximum intensity projection...")
log
.
debug
(
"
Creating maximum intensity projection...
"
)
proj
=
ZProjector
.
run
(
imp
,
"
max
"
)
return
proj
...
...
@@ -64,7 +65,7 @@ def create_and_save(imp, projections, path, filename, export_format):
'
Sum
'
:
'
sum
'
,
}
for
projection
in
projections
:
#
log.debug("Creating '%s' projection..."
%
projection)
log
.
debug
(
"
Creating
'
%s
'
projection...
"
,
projection
)
proj
=
ZProjector
.
run
(
imp
,
command
[
projection
])
export_using_orig_name
(
proj
,
path
,
filename
,
...
...
This diff is collapsed.
Click to expand it.
src/imcflibs/imagej/shading.py
+
3
−
1
View file @
eabdfcf8
...
...
@@ -5,6 +5,7 @@ import os
from
..imagej
import
bioformats
from
..imagej
import
projections
from
..pathtools
import
listdir_matching
from
..log
import
LOG
as
log
from
ij
import
IJ
from
ij.plugin
import
ImageCalculator
,
RGBStackMerge
...
...
@@ -70,6 +71,7 @@ def correct_and_project(filename, path, model, proj, fmt):
The file format suffix to be used for the results and projections, e.g.
'
.ics
'
for ICS2 etc. See the Bio-Formats specification for details.
"""
log
.
debug
(
"
Processing [%s]...
"
,
filename
)
if
not
os
.
path
.
exists
(
path
):
os
.
makedirs
(
path
)
...
...
@@ -87,7 +89,7 @@ def correct_and_project(filename, path, model, proj, fmt):
# corrected.show()
corrected
.
close
()
#
log.debug("Done processing [%s]
" %
os.path.basename(
in_
file))
log
.
debug
(
"
Done processing [%s]
.
"
,
os
.
path
.
basename
(
fil
enam
e
))
def
process_folder
(
path
,
suffix
,
outpath
,
model_file
,
fmt
):
...
...
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