Blackenize code

src/imcflibs/__init__.py

@@ -21,4 +21,4 @@ Biozentrum, University of Basel, Switzerland.
 [imagej]: https://imagej.net
 """
 
-__version__ = '${project.version}'
+__version__ = "${project.version}"

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)

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.
 

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

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()

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]

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

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)

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

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

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