diff --git a/src/imcflibs/__init__.py b/src/imcflibs/__init__.py
index 16c39bca9f7cd1f32daeb8fb645cde0308d186c9..3b59a6fd781f93d8605357a582adeaeb04ad9dd1 100644
--- a/src/imcflibs/__init__.py
+++ b/src/imcflibs/__init__.py
@@ -21,4 +21,4 @@ Biozentrum, University of Basel, Switzerland.
[imagej]: https://imagej.net
"""
-__version__ = '${project.version}'
+__version__ = "${project.version}"
diff --git a/src/imcflibs/imagej/misc.py b/src/imcflibs/imagej/misc.py
index 2d0e33e3ab23dbbc6128d7faa5f3040e03f5491f..17620077ff1f479647d380a1cf2c44a913c51629 100644
--- a/src/imcflibs/imagej/misc.py
+++ b/src/imcflibs/imagej/misc.py
@@ -15,9 +15,10 @@ def show_status(msg):
def show_progress(cur, final):
"""Wrapper to update the progress bar and issue a log message."""
# ij.IJ.showProgress is adding 1 to the value given as first parameter...
- log.info("Progress: %s / %s (%s)", cur+1, final, (1.0+cur)/final)
+ log.info("Progress: %s / %s (%s)", cur + 1, final, (1.0 + cur) / final)
IJ.showProgress(cur, final)
+
def error_exit(msg):
"""Convenience wrapper to log an error and exit then."""
log.error(msg)
diff --git a/src/imcflibs/imagej/prefs.py b/src/imcflibs/imagej/prefs.py
index 54e51f45e28466f68822325b625039b83f0d49dc..179907c5d4830c8558fe4fb435f6ae0500fb047a 100644
--- a/src/imcflibs/imagej/prefs.py
+++ b/src/imcflibs/imagej/prefs.py
@@ -2,6 +2,7 @@
from ij import Prefs # pylint: disable-msg=E0401
+
def debug_mode():
"""Wrapper to check if 'imcf.debugging' is enabled.
diff --git a/src/imcflibs/imagej/projections.py b/src/imcflibs/imagej/projections.py
index 6313875f3011a5b1066bd8b2c8b15ba7d76a31f1..1a6d0501f8edd77d909f0d624dc258e3566097c2 100644
--- a/src/imcflibs/imagej/projections.py
+++ b/src/imcflibs/imagej/projections.py
@@ -82,18 +82,21 @@ def create_and_save(imp, projections, path, filename, export_format):
return False
command = {
- 'Average': 'avg',
- 'Maximum': 'max',
- 'Sum': 'sum',
+ "Average": "avg",
+ "Maximum": "max",
+ "Sum": "sum",
}
for projection in projections:
log.debug("Creating '%s' projection...", projection)
proj = ZProjector.run(imp, command[projection])
- export_using_orig_name(proj,
- path, filename,
- "-%s" % command[projection],
- export_format,
- overwrite=True)
+ export_using_orig_name(
+ proj,
+ path,
+ filename,
+ "-%s" % command[projection],
+ export_format,
+ overwrite=True,
+ )
proj.close()
return True
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index c0a20a3ece44c5f1ea51557380cde8bbcbc65412..ab59777fb3572485eea81e2214b2f1b08129f992 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -105,10 +105,10 @@ def correct_and_project(filename, path, model, proj, fmt):
imps = [imp]
ret_corr = True
- if proj == 'None':
+ if proj == "None":
projs = []
- elif proj == 'ALL':
- projs = ['Average', 'Maximum']
+ elif proj == "ALL":
+ projs = ["Average", "Maximum"]
else:
projs = [proj]
for imp in imps:
@@ -159,8 +159,7 @@ def process_files(files, outpath, model_file, fmt):
fmt : str
The file format suffix for storing the results.
"""
- log.info("Running shading correction and projections on %s files...",
- len(files))
+ log.info("Running shading correction and projections on %s files...", len(files))
if model_file.upper() in ["-", "NONE"]:
model = None
@@ -177,7 +176,7 @@ def process_files(files, outpath, model_file, fmt):
misc.error_exit("Opening shading model [%s] failed!" % model_file)
for in_file in files:
- correct_and_project(in_file, outpath, model, 'ALL', fmt)
+ correct_and_project(in_file, outpath, model, "ALL", fmt)
if model:
model.close()
diff --git a/src/imcflibs/imagej/split.py b/src/imcflibs/imagej/split.py
index 8aa15b0b54e801181c549c842137b9f98c7bad99..5184e91b8234f5535e35495548dd1d7dcc61d126 100644
--- a/src/imcflibs/imagej/split.py
+++ b/src/imcflibs/imagej/split.py
@@ -6,6 +6,7 @@ from ij import IJ, ImagePlus # pylint: disable-msg=E0401
from ij.io import FileSaver # pylint: disable-msg=E0401
from ij.plugin import ChannelSplitter # pylint: disable-msg=E0401
+
def split_by_c_and_z(log, dname, imgf, skip_top, skip_bottom):
"""Helper function to open, split and save a file.
@@ -36,7 +37,7 @@ def split_by_c_and_z(log, dname, imgf, skip_top, skip_bottom):
if not os.path.isdir(tgt_dir):
os.mkdir(tgt_dir)
stack = channel.getStack()
- for z in range(1+skip_top, stack.getSize()+1-skip_bottom):
+ for z in range(1 + skip_top, stack.getSize() + 1 - skip_bottom):
proc = stack.getProcessor(z)
fout = "%s/%s-z%s%s" % (tgt_dir, fname[0], z, fname[1])
# fout = dname + "/" + c_name + "/" + fname[0] + "-z" + z + fname[1]
diff --git a/src/imcflibs/imagej/stitching.py b/src/imcflibs/imagej/stitching.py
index 29fd30b4194a0e320d15163e5e9e79189baec505..a82a66d228566c455871d6a11eb02d1d5b3d91d8 100644
--- a/src/imcflibs/imagej/stitching.py
+++ b/src/imcflibs/imagej/stitching.py
@@ -26,12 +26,12 @@ def process_fluoview_project(infile):
micrometa.experiment.MosaicExperiment
The mosaic object if parsing the project file has been successful.
"""
- if infile[-9:] == '.omp2info':
+ if infile[-9:] == ".omp2info":
mosaicclass = micrometa.fluoview.FluoView3kMosaic
- elif infile[-4:] == '.log':
+ elif infile[-4:] == ".log":
mosaicclass = micrometa.fluoview.FluoViewMosaic
else:
- error_exit('Unsupported input file: %s' % infile)
+ error_exit("Unsupported input file: %s" % infile)
log.info("Parsing project file: [%s]", infile)
ij.IJ.showStatus("Parsing mosaics...")
@@ -41,15 +41,15 @@ def process_fluoview_project(infile):
ij.IJ.showProgress(0.0)
show_status("Parsed %s / %s mosaics" % (0, total))
for i, subtree in enumerate(mosaics.mosaictrees):
- log.info("Parsing mosaic %s...", i+1)
+ log.info("Parsing mosaic %s...", i + 1)
try:
mosaics.add_mosaic(subtree, i)
except (ValueError, IOError) as err:
- log.warn('Skipping mosaic %s: %s', i, err)
+ log.warn("Skipping mosaic %s: %s", i, err)
except RuntimeError as err:
- log.warn('Error parsing mosaic %s, SKIPPING: %s', i, err)
+ log.warn("Error parsing mosaic %s, SKIPPING: %s", i, err)
show_progress(i, total)
- show_status("Parsed %s / %s mosaics" % (i+1, total))
+ show_status("Parsed %s / %s mosaics" % (i + 1, total))
show_progress(total, total)
show_status("Parsed %i mosaics." % total)
@@ -79,30 +79,30 @@ def gen_macro(mosaics, indir, outfile=None, opts=None):
list(str)
The generated macro code as a list of strings (one str per line).
"""
- templates = join(getProperty('fiji.dir'), 'jars', 'python-micrometa.jar')
+ templates = join(getProperty("fiji.dir"), "jars", "python-micrometa.jar")
log.info("Using macro templates from [%s].", templates)
log.info("Using [%s] as base directory.", indir)
# set the default stitcher options
stitcher_options = {
- 'export_format': '".ids"',
- 'split_z_slices': 'false',
- 'rotation_angle': 0,
- 'stitch_regression': 0.3,
- 'stitch_maxavg_ratio': 2.5,
- 'stitch_abs_displace': 3.5,
- 'compute' : 'false',
+ "export_format": '".ids"',
+ "split_z_slices": "false",
+ "rotation_angle": 0,
+ "stitch_regression": 0.3,
+ "stitch_maxavg_ratio": 2.5,
+ "stitch_abs_displace": 3.5,
+ "compute": "false",
}
# merge explicit options, overriding the defaults from above if applicable:
if opts:
stitcher_options.update(opts)
code = micrometa.imagej.gen_stitching_macro(
- name=mosaics.infile['dname'],
+ name=mosaics.infile["dname"],
path=indir,
- tplpfx='templates/imagej-macro/stitching',
+ tplpfx="templates/imagej-macro/stitching",
tplpath=templates,
- opts=stitcher_options
+ opts=stitcher_options,
)
log.debug("============= begin of generated macro code =============")
@@ -110,7 +110,7 @@ def gen_macro(mosaics, indir, outfile=None, opts=None):
log.debug("============= end of generated macro code =============")
if outfile is not None:
- log.info('Writing stitching macro.')
+ log.info("Writing stitching macro.")
micrometa.imagej.write_stitching_macro(code, outfile)
return code
diff --git a/src/imcflibs/iotools.py b/src/imcflibs/iotools.py
index 6c5a955ff95f327f1d6a3ef9dcdf679ae7d6403a..9d0d44c483b4e822631796905b3ff76b2ae4ab54 100644
--- a/src/imcflibs/iotools.py
+++ b/src/imcflibs/iotools.py
@@ -7,7 +7,7 @@ from .log import LOG as log
from .strtools import flatten
-def filehandle(fname, mode='r'):
+def filehandle(fname, mode="r"):
"""Make sure a variable is either a filehandle or create one from it.
This function takes a variable and checks whether it is already a
@@ -41,13 +41,13 @@ def filehandle(fname, mode='r'):
<type 'file'>
"""
log.debug(type(fname))
- if type(fname).__name__ == 'str':
+ if type(fname).__name__ == "str":
try:
return open(fname, mode)
except IOError as err:
message = "can't open '%s': %s"
raise SystemExit(message % (fname, err))
- elif type(fname).__name__ == 'file':
+ elif type(fname).__name__ == "file":
if fname.mode != mode:
message = "mode mismatch: %s != %s"
raise IOError(message % (fname.mode, mode))
@@ -57,7 +57,7 @@ def filehandle(fname, mode='r'):
raise SystemExit(message % type(fname))
-def readtxt(fname, path='', flat=False):
+def readtxt(fname, path="", flat=False):
"""Commodity function for reading text files plain or zipped.
Read a text file line by line either plainly from a directory or a .zip or
@@ -90,13 +90,13 @@ def readtxt(fname, path='', flat=False):
"""
zipread = None
suffix = splitext(path)[1].lower()
- if ((suffix == '.zip') or (suffix == '.jar')):
+ if (suffix == ".zip") or (suffix == ".jar"):
# ZipFile only works as a context manager from Python 2.7 on
# tag:python25
- zipread = zipfile.ZipFile(path, 'r')
+ zipread = zipfile.ZipFile(path, "r")
fin = zipread.open(fname)
else:
- fin = open(join(path, fname), 'r')
+ fin = open(join(path, fname), "r")
txt = fin.readlines() # returns file as a list, one entry per line
if flat:
txt = flatten(txt)
diff --git a/src/imcflibs/log.py b/src/imcflibs/log.py
index 2d9682014d28c2de0ab209e0c88b132962b73d89..4b0b967df2da5da350943dc271860a7fff232c81 100644
--- a/src/imcflibs/log.py
+++ b/src/imcflibs/log.py
@@ -38,7 +38,7 @@ def enable_console_logging():
return stream_handler
-def enable_file_logging(fname, mode='a'):
+def enable_file_logging(fname, mode="a"):
"""Add a logging handler writing to a file.
Returns
diff --git a/src/imcflibs/pathtools.py b/src/imcflibs/pathtools.py
index da45be71e1f80cd6b34fafeead1a7d6a1f2314f2..7007fbb1eabd05948cd92a787000cbb85281893b 100644
--- a/src/imcflibs/pathtools.py
+++ b/src/imcflibs/pathtools.py
@@ -53,13 +53,13 @@ def parse_path(path):
''
"""
parsed = {}
- parsed['orig'] = path
- path = path.replace('\\', sep)
- parsed['full'] = path
- parsed['path'] = os.path.dirname(path) + sep
- parsed['fname'] = os.path.basename(path)
- parsed['dname'] = os.path.basename(os.path.dirname(parsed['path']))
- parsed['ext'] = os.path.splitext(parsed['fname'])[1]
+ parsed["orig"] = path
+ path = path.replace("\\", sep)
+ parsed["full"] = path
+ parsed["path"] = os.path.dirname(path) + sep
+ parsed["fname"] = os.path.basename(path)
+ parsed["dname"] = os.path.basename(os.path.dirname(parsed["path"]))
+ parsed["ext"] = os.path.splitext(parsed["fname"])[1]
return parsed
@@ -130,7 +130,7 @@ def image_basename(orig_name):
'FoObAr'
"""
base = os.path.splitext(os.path.basename(orig_name))[0]
- if base.lower().endswith('.ome'):
+ if base.lower().endswith(".ome"):
base = base[:-4]
return base
@@ -190,10 +190,11 @@ def derive_out_dir(in_dir, out_dir):
# pylint: disable-msg=C0103
# we use the variable name 'exists' in its common spelling (lowercase), so
# removing this workaround will be straightforward at a later point
-if platform.python_implementation() == 'Jython':
+if platform.python_implementation() == "Jython":
# pylint: disable-msg=F0401
# java.lang is only importable within Jython, pylint would complain
import java.lang
+
exists = jython_fiji_exists
else:
exists = os.path.exists
diff --git a/src/imcflibs/strtools.py b/src/imcflibs/strtools.py
index 2f1c6269ab20d4f050c9e9f960116e085b658328..ecbb79048258c98261f70dc1fc8837481753f83c 100644
--- a/src/imcflibs/strtools.py
+++ b/src/imcflibs/strtools.py
@@ -18,7 +18,7 @@ def _is_string_like(obj):
False
"""
try:
- obj + ''
+ obj + ""
except (TypeError, ValueError):
return False
return True
@@ -95,5 +95,5 @@ def strip_prefix(string, prefix):
string doesn't start with the prefix, it is returned unchanged.
"""
if string.startswith(prefix):
- string = string[len(prefix):]
+ string = string[len(prefix) :]
return string