formatting fixes

affogato_comparison.py

@@ -1,5 +1,4 @@
 import numpy as np
-import pytest
 
 import mwatershed
 
@@ -22,4 +21,4 @@
 components = compute_mws_segmentation_from_affinities(affinities, offsets, 0)
 t4 = time.time()
 
-print(f"AFFOGATO: {len(np.unique(components))} components in {t4-t3} seconds")
+print(f"AFFOGATO: {len(np.unique(components))} components in {t4-t3} seconds")

docs/conf.py

@@ -20,7 +20,8 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 import mwatershed
 
@@ -32,24 +33,24 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u"""mwatershed"""
-copyright = u"""2023, William Hunter Patton"""
-author = u"""William Hunter Patton"""
+project = """mwatershed"""
+copyright = """2023, William Hunter Patton"""
+author = """William Hunter Patton"""
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -70,10 +71,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -84,7 +85,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -95,13 +96,13 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mwatersheddoc'
+htmlhelp_basename = "mwatersheddoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -110,15 +111,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -128,21 +126,21 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, """mwatershed.tex""",
-     u"""mwatershed Documentation""",
-     u"""William Hunter Patton""", 'manual'),
+    (
+        master_doc,
+        """mwatershed.tex""",
+        """mwatershed Documentation""",
+        """William Hunter Patton""",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'mwatershed',
-     u'mwatershed Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "mwatershed", "mwatershed Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -151,13 +149,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'mwatershed',
-     u'mwatershed Documentation',
-     author,
-     'mwatershed',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "mwatershed",
+        "mwatershed Documentation",
+        author,
+        "mwatershed",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
-
-
-

fun.py

@@ -0,0 +1,26 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import mwatershed
+
+# Generate an empty ndarray of labels
+labels = np.zeros((100, 100))
+
+# Add circles with different labels
+labels[25:40, 25:40] = 1
+labels[60:75, 60:75] = 2
+labels[50:70, 10:30] = 3
+
+affs = np.zeros((2, 100, 100))
+# affs[0] = labels > 0
+# affs[1] = labels > 0
+affs[0, 0, 0] = 1
+
+result = mwatershed.agglom(affs - 0.5, [[0, 1], [1, 0]]).astype(np.uint32)
+print(result.min(), result.max())
+
+fig, ax = plt.subplots(1, 3, figsize=(10, 5))
+# Plot the labels using imshow
+ax[0].imshow(labels)
+ax[1].imshow(affs[0])
+ax[2].imshow(result)
+plt.show()

tests/test_mwatershed.py

@@ -1,5 +1,4 @@
 import numpy as np
-import pytest
 
 import mwatershed