senoquant 1.0.0b1__py3-none-any.whl

senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/utils/utils.py

@@ -0,0 +1,272 @@
+from __future__ import print_function, unicode_literals, absolute_import, division
+
+import os
+import numpy as np
+import json
+import collections
+import platform
+import random
+from six.moves import range, zip, map, reduce, filter
+from .six import Path
+
+###
+
+
+def is_tf_backend():
+    from .tf import BACKEND as K
+    return K.backend() == 'tensorflow'
+
+
+def backend_channels_last():
+    from .tf import BACKEND as K
+    assert K.image_data_format() in ('channels_first','channels_last')
+    return K.image_data_format() == 'channels_last'
+
+
+def move_channel_for_backend(X,channel):
+    if backend_channels_last():
+        return np.moveaxis(X, channel, -1)
+    else:
+        return np.moveaxis(X, channel,  1)
+
+
+###
+
+
+def load_json(fpath):
+    with open(fpath,'r') as f:
+        return json.load(f)
+
+
+def save_json(data,fpath,**kwargs):
+    with open(fpath,'w') as f:
+        f.write(json.dumps(data,**kwargs))
+
+
+###
+
+
+def normalize(x, pmin=3, pmax=99.8, axis=None, clip=False, eps=1e-20, dtype=np.float32):
+    """Percentile-based image normalization."""
+
+    mi = np.percentile(x,pmin,axis=axis,keepdims=True)
+    ma = np.percentile(x,pmax,axis=axis,keepdims=True)
+    return normalize_mi_ma(x, mi, ma, clip=clip, eps=eps, dtype=dtype)
+
+
+def normalize_mi_ma(x, mi, ma, clip=False, eps=1e-20, dtype=np.float32):
+    if dtype is not None:
+        x   = x.astype(dtype,copy=False)
+        mi  = dtype(mi) if np.isscalar(mi) else mi.astype(dtype,copy=False)
+        ma  = dtype(ma) if np.isscalar(ma) else ma.astype(dtype,copy=False)
+        eps = dtype(eps)
+
+    try:
+        import numexpr
+        x = numexpr.evaluate("(x - mi) / ( ma - mi + eps )")
+    except ImportError:
+        x =                   (x - mi) / ( ma - mi + eps )
+
+    if clip:
+        x = np.clip(x,0,1)
+
+    return x
+
+
+def normalize_minmse(x, target):
+    """Affine rescaling of x, such that the mean squared error to target is minimal."""
+    cov = np.cov(x.flatten(),target.flatten())
+    alpha = cov[0,1] / (cov[0,0]+1e-10)
+    beta = target.mean() - alpha*x.mean()
+    return alpha*x + beta
+
+
+###
+
+
+def _raise(e):
+    if isinstance(e, BaseException):
+        raise e
+    else:
+        raise ValueError(e)
+
+
+# https://docs.python.org/3/library/itertools.html#itertools-recipes
+def consume(iterator):
+    collections.deque(iterator, maxlen=0)
+
+
+def compose(*funcs):
+    return lambda x: reduce(lambda f,g: g(f), funcs, x)
+
+
+###
+
+
+def download_and_extract_zip_file(url, targetdir='.', verbose=True):
+    import csv
+    from six.moves.urllib.request import urlretrieve
+    from six.moves.urllib.parse import urlparse
+    from zipfile import ZipFile
+
+    res = urlparse(url)
+    if res.scheme in ('','file'):
+        url = Path(res.path).resolve().as_uri()
+        # local file, 'urlretrieve' will not make a copy
+        # -> don't delete 'downloaded' file
+        delete = False
+    else:
+        delete = True
+
+    # verbosity levels:
+    # - 0: no messages
+    # - 1: status messages
+    # - 2: status messages and list of all files
+    if isinstance(verbose,bool):
+        verbose *= 2
+
+    log = (print) if verbose else (lambda *a,**k: None)
+
+    targetdir = Path(targetdir)
+    if not targetdir.is_dir():
+        targetdir.mkdir(parents=True,exist_ok=True)
+
+    provided = []
+
+    def content_is_missing():
+        try:
+            filepath, http_msg = urlretrieve(url+'.contents')
+            with open(filepath,'r') as contents_file:
+                contents = list(csv.reader(contents_file,delimiter='\t'))
+        except:
+            return True
+        finally:
+            if delete:
+                try: os.unlink(filepath)
+                except: pass
+
+        for size, relpath in contents:
+            size, relpath = int(size.strip()), relpath.strip()
+            entry = targetdir / relpath
+            if not entry.exists():
+                return True
+            if entry.is_dir():
+                if not relpath.endswith('/'): return True
+            elif entry.is_file():
+                if relpath.endswith('/') or entry.stat().st_size != size: return True
+            else:
+                return True
+            provided.append(relpath)
+
+        return False
+
+
+    if content_is_missing():
+        try:
+            log('Files missing, downloading...',end='')
+            filepath, http_msg = urlretrieve(url)
+            with ZipFile(filepath,'r') as zip_file:
+                log(' extracting...',end='')
+                zip_file.extractall(str(targetdir))
+                provided = zip_file.namelist()
+            log(' done.')
+        finally:
+            if delete:
+                try: os.unlink(filepath)
+                except: pass
+    else:
+        log('Files found, nothing to download.')
+
+    if verbose > 1:
+        log('\n'+str(targetdir)+':')
+        consume(map(lambda x: log('-',Path(x)), provided))
+
+
+###
+
+
+def axes_check_and_normalize(axes,length=None,disallowed=None,return_allowed=False):
+    """
+    S(ample), T(ime), C(hannel), Z, Y, X
+    """
+    allowed = 'STCZYX'
+    axes is not None or _raise(ValueError('axis cannot be None.'))
+    axes = str(axes).upper()
+    consume(a in allowed or _raise(ValueError("invalid axis '%s', must be one of %s."%(a,list(allowed)))) for a in axes)
+    disallowed is None or consume(a not in disallowed or _raise(ValueError("disallowed axis '%s'."%a)) for a in axes)
+    consume(axes.count(a)==1 or _raise(ValueError("axis '%s' occurs more than once."%a)) for a in axes)
+    length is None or len(axes)==length or _raise(ValueError('axes (%s) must be of length %d.' % (axes,length)))
+    return (axes,allowed) if return_allowed else axes
+
+
+def axes_dict(axes):
+    """
+    from axes string to dict
+    """
+    axes, allowed = axes_check_and_normalize(axes,return_allowed=True)
+    return { a: None if axes.find(a) == -1 else axes.find(a) for a in allowed }
+    # return collections.namedtuple('Axes',list(allowed))(*[None if axes.find(a) == -1 else axes.find(a) for a in allowed ])
+
+
+def move_image_axes(x, fr, to, adjust_singletons=False):
+    """
+    x: ndarray
+    fr,to: axes string (see `axes_dict`)
+    """
+    fr = axes_check_and_normalize(fr, length=x.ndim)
+    to = axes_check_and_normalize(to)
+
+    fr_initial = fr
+    x_shape_initial = x.shape
+    adjust_singletons = bool(adjust_singletons)
+    if adjust_singletons:
+        # remove axes not present in 'to'
+        slices = [slice(None) for _ in x.shape]
+        for i,a in enumerate(fr):
+            if (a not in to) and (x.shape[i]==1):
+                # remove singleton axis
+                slices[i] = 0
+                fr = fr.replace(a,'')
+        x = x[tuple(slices)]
+        # add dummy axes present in 'to'
+        for i,a in enumerate(to):
+            if (a not in fr):
+                # add singleton axis
+                x = np.expand_dims(x,-1)
+                fr += a
+
+    if set(fr) != set(to):
+        _adjusted = '(adjusted to %s and %s) ' % (x.shape, fr) if adjust_singletons else ''
+        raise ValueError(
+            'image with shape %s and axes %s %snot compatible with target axes %s.'
+            % (x_shape_initial, fr_initial, _adjusted, to)
+        )
+
+    ax_from, ax_to = axes_dict(fr), axes_dict(to)
+    if fr == to:
+        return x
+    return np.moveaxis(x, [ax_from[a] for a in fr], [ax_to[a] for a in fr])
+
+
+###
+
+
+def choice(population, k=1, replace=True):
+    ver = platform.sys.version_info
+    if replace and (ver.major,ver.minor) in [(2,7),(3,5)]: # python 2.7 or 3.5
+        # slow if population is large and not a np.ndarray
+        return list(np.random.choice(population, k, replace=replace))
+    else:
+        try:
+            # save state of 'random' and set seed using 'np.random'
+            state = random.getstate()
+            random.seed(int(np.random.randint(0, np.iinfo(np.uint32).max, dtype=np.uint32)))
+            if replace:
+                # sample with replacement
+                return random.choices(population, k=k)
+            else:
+                # sample without replacement
+                return random.sample(population, k=k)
+        finally:
+            # restore state of 'random'
+            random.setstate(state)

senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/csbdeep/version.py

@@ -0,0 +1 @@
+__version__ = '0.8.2'

senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/docs/source/conf.py

@@ -0,0 +1,368 @@
+# -*- coding: utf-8 -*-
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+from datetime import datetime
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# 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.napoleon',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    # 'sphinx.ext.doctest',
+    'sphinx.ext.viewcode',
+    # 'sphinx.ext.linkcode',
+]
+
+def linkcode_resolve(domain, info):
+    if domain != 'py':
+        return None
+    if not info['module']:
+        return None
+    filename = info['module'].replace('.', '/')
+    return "https://github.com/csbdeep/csbdeep/tree/main/%s.py" % filename
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'CSBDeep'
+copyright = u'2018–{}, CSBD'.format(datetime.now().year)
+author = u'Uwe Schmidt, Martin Weigert'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+# version = u'0.1.0'
+# The full version, including alpha/beta/rc tags.
+# release = u'0.1.0'
+from csbdeep import __version__ as version
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+# todo_include_todos = True
+
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
+                       'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+                       'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+                       'matplotlib': ('https://matplotlib.org/', None),
+                       # 'keras': ('https://keras.io/', None), # doesn't work for keras
+                       }
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+
+# 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
+# documentation.
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+html_sidebars = {
+    '**': [
+        'about.html',
+        #'linkbar.html',
+        'navigation.html',
+        #'relations.html',
+        'searchbox.html',
+    ]
+}
+
+
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = False
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
+#html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# Now only 'ja' uses this config value
+#html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'csbdeepdoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+'papersize': 'a4paper',
+
+# The font size ('10pt', '11pt' or '12pt').
+'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+
+# Latex figure (float) alignment
+#'figure_align': 'htbp',
+}
+
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+
+latex_toplevel_sectioning = "section"
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+epub_author = author
+epub_publisher = author
+epub_copyright = copyright
+
+# The basename for the epub file. It defaults to the project name.
+#epub_basename = project
+
+# The HTML theme for the epub output. Since the default themes are not
+# optimized for small screen space, using the same theme for HTML and epub
+# output is usually not wise. This defaults to 'epub', a theme designed to save
+# visual space.
+#epub_theme = 'epub'
+
+# The language of the text. It defaults to the language option
+# or 'en' if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# A sequence of (type, uri, title) tuples for the guide element of content.opf.
+#epub_guide = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files that should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+# Choose between 'default' and 'includehidden'.
+#epub_tocscope = 'default'
+
+# Fix unsupported image types using the Pillow.
+#epub_fix_images = False
+
+# Scale large images.
+#epub_max_image_width = 0
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#epub_show_urls = 'inline'
+
+# If false, no index is generated.
+#epub_use_index = True

senoquant/tabs/segmentation/stardist_onnx_utils/_csbdeep/setup.py

@@ -0,0 +1,68 @@
+from __future__ import absolute_import
+from setuptools import setup, find_packages
+from os import path
+
+_dir = path.abspath(path.dirname(__file__))
+
+with open(path.join(_dir,'csbdeep','version.py')) as f:
+    exec(f.read())
+
+with open(path.join(_dir,'README.md')) as f:
+    long_description = f.read()
+
+
+setup(name='csbdeep',
+      version=__version__,
+      description='CSBDeep - a toolbox for Content-aware Image Restoration (CARE)',
+      long_description=long_description,
+      long_description_content_type='text/markdown',
+      url='http://csbdeep.bioimagecomputing.com/',
+      author='Uwe Schmidt, Martin Weigert',
+      author_email='research@uweschmidt.org, martin.weigert@epfl.ch',
+      license='BSD 3-Clause License',
+      packages=find_packages(),
+      python_requires='>=3.6',
+
+      project_urls={
+          'Documentation': 'http://csbdeep.bioimagecomputing.com/doc/',
+          'Repository': 'https://github.com/csbdeep/csbdeep',
+      },
+
+      classifiers=[
+          'Development Status :: 4 - Beta',
+          'Intended Audience :: Science/Research',
+          'Topic :: Scientific/Engineering',
+          'License :: OSI Approved :: BSD License',
+
+          'Programming Language :: Python :: 3.6',
+          'Programming Language :: Python :: 3.7',
+          'Programming Language :: Python :: 3.8',
+          'Programming Language :: Python :: 3.9',
+          'Programming Language :: Python :: 3.10',
+          'Programming Language :: Python :: 3.11',
+          'Programming Language :: Python :: 3.12',
+          'Programming Language :: Python :: 3.13',
+      ],
+
+      install_requires=[
+          "numpy",
+          "scipy",
+          "matplotlib",
+          "six",
+          "tifffile",
+          "tqdm",
+          "packaging",
+      ],
+
+      extras_require={
+          "tf1":  ["keras>=2.1.2,<2.4","protobuf<3.21","h5py<3","numpy<2"],
+          "test": ["pytest"],
+          "docs": ["sphinx","sphinx-rtd-theme"],
+      },
+
+      entry_points={
+          'console_scripts': [
+              'care_predict = csbdeep.scripts.care_predict:main'
+          ]
+      }
+)