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imcf
python-imcflibs
Commits
14106fe0
Commit
14106fe0
authored
6 years ago
by
Niko Ehrenfeuchter
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Re-activate logging calls in imagej.bioformats
parent
8c58cd2b
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1 changed file
src/imcflibs/imagej/bioformats.py
+5
-3
5 additions, 3 deletions
src/imcflibs/imagej/bioformats.py
with
5 additions
and
3 deletions
src/imcflibs/imagej/bioformats.py
+
5
−
3
View file @
14106fe0
...
@@ -14,6 +14,7 @@ from loci.plugins import BF
...
@@ -14,6 +14,7 @@ from loci.plugins import BF
from
loci.plugins.in
import
ImporterOptions
from
loci.plugins.in
import
ImporterOptions
from
..pathtools
import
image_basename
from
..pathtools
import
image_basename
from
..log
import
LOG
as
log
def
import_image
(
filename
,
def
import_image
(
filename
,
...
@@ -52,7 +53,7 @@ def import_image(filename,
...
@@ -52,7 +53,7 @@ def import_image(filename,
options
.
setSplitFocalPlanes
(
split_z
)
options
.
setSplitFocalPlanes
(
split_z
)
options
.
setSplitTimepoints
(
split_t
)
options
.
setSplitTimepoints
(
split_t
)
options
.
setId
(
filename
)
options
.
setId
(
filename
)
#
log.info("Reading [%s]"
%
filename)
log
.
info
(
"
Reading [%s]
"
,
filename
)
orig_imps
=
BF
.
openImagePlus
(
options
)
orig_imps
=
BF
.
openImagePlus
(
options
)
return
orig_imps
return
orig_imps
...
@@ -70,14 +71,15 @@ def export(imp, filename, overwrite=False):
...
@@ -70,14 +71,15 @@ def export(imp, filename, overwrite=False):
A switch to indicate existing files should be overwritten. Default is to
A switch to indicate existing files should be overwritten. Default is to
keep existing files, in this case an IOError is raised.
keep existing files, in this case an IOError is raised.
"""
"""
#
log.info("Exporting to [%s]"
% out_fil
e)
log
.
info
(
"
Exporting to [%s]
"
,
filenam
e
)
if
os
.
path
.
exists
(
filename
):
if
os
.
path
.
exists
(
filename
):
if
not
overwrite
:
if
not
overwrite
:
raise
IOError
(
'
file [%s] already exists!
'
%
filename
)
raise
IOError
(
'
file [%s] already exists!
'
%
filename
)
log
.
debug
(
"
Removing existing file [%s]...
"
,
filename
)
os
.
remove
(
filename
)
os
.
remove
(
filename
)
IJ
.
run
(
imp
,
"
Bio-Formats Exporter
"
,
"
save=[
"
+
filename
+
"
]
"
)
IJ
.
run
(
imp
,
"
Bio-Formats Exporter
"
,
"
save=[
"
+
filename
+
"
]
"
)
#
log.debug("Exporting finished.")
log
.
debug
(
"
Exporting finished.
"
)
def
export_using_orig_name
(
imp
,
path
,
orig_name
,
tag
,
suffix
,
overwrite
=
False
):
def
export_using_orig_name
(
imp
,
path
,
orig_name
,
tag
,
suffix
,
overwrite
=
False
):
...
...
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