Update doc

algotom/io/converter.py

@@ -22,8 +22,8 @@
 
 """
 Module for converting data type:
-- Convert a list of tif files to a hdf/nxs file.
-- Extract tif images from a hdf/nxs file.
+    - Convert a list of tif files to a hdf/nxs file.
+    - Extract tif images from a hdf/nxs file.
 """
 
 import os

algotom/io/loadersaver.py

@@ -22,12 +22,12 @@
 
 """
 Module for I/O tasks:
-- Load data from an image file (tif, png, jpeg) or a hdf/nxs file.
-- Get dataset information in a hdf/nxs file.
-- Search for datasets in a hdf/nxs file.
-- Save a 2D array as a tif image or 2D, 3D array to a hdf/nxs file.
-- Search file names, make a file/folder name.
-- Load distortion coefficients from a txt file.
+    - Load data from an image file (tif, png, jpeg) or a hdf/nxs file.
+    - Get dataset information in a hdf/nxs file.
+    - Search for datasets in a hdf/nxs file.
+    - Save a 2D array as a tif image or 2D, 3D array to a hdf/nxs file.
+    - Search file names, make a file/folder name.
+    - Load distortion coefficients from a txt file.
 """
 
 import os

algotom/post/postprocessing.py

@@ -22,11 +22,11 @@
 
 """
 Module of methods in the postprocessing stage:
-- Get statistical information of reconstructed images or a dataset.
-- Downsample 2D, 3D array, or a dataset.
-- Rescale 2D, 3D array or a dataset to 8-bit or 16-bit data-type.
-- Removing ring artifacts in a reconstructed image by transform back and forth
-between the polar coordinates and the Cartesian coordinates.
+    - Get statistical information of reconstructed images or a dataset.
+    - Downsample 2D, 3D array, or a dataset.
+    - Rescale 2D, 3D array or a dataset to 8-bit or 16-bit data-type.
+    - Removing ring artifacts in a reconstructed image by transform back and
+      forth between the polar coordinates and the Cartesian coordinates.
 """
 
 import os

algotom/prep/calculation.py

@@ -22,16 +22,16 @@
 
 """
 Module of calculation methods in the preprocessing stage:
-- Calculating the center-of-rotation (COR) in a 180-degree scan using a
-  sinogram.
-- Determining the overlap-side and overlap-area between images.
-- Calculating the COR in a half-acquisition scan (360-degree scan with offset
-  COR).
-- Using the similar technique as above to calculate the COR in a 180-degree scan
-  from two projections.
-- Determining the relative translations between images using phase-correlation
-  technique.
-- Calculating the COR in a 180-degree scan using phase-correlation technique.
+    - Calculating the center-of-rotation (COR) in a 180-degree scan using a
+      sinogram.
+    - Determining the overlap-side and overlap-area between images.
+    - Calculating the COR in a half-acquisition scan (360-degree scan with
+      offset COR).
+    - Using the similar technique as above to calculate the COR in a 180-degree
+      scan from two projections.
+    - Determining the relative translations between images using
+      phase-correlation technique.
+    - Calculating the COR in a 180-degree scan using phase-correlation technique.
 """
 
 import numpy as np

algotom/prep/conversion.py

@@ -22,14 +22,14 @@
 
 """
 Module of conversion methods in the preprocessing stage:
-- Stitching images.
-- Joining images if there is no overlapping.
-- Converting a 360-degree sinogram with offset center-of-rotation (COR) to
-  a 180-degree sinogram.
-- Extending a 360-degree sinogram with offset COR for direct reconstruction
-  instead of converting it to a 180-degree sinogram.
-- Converting a 180-degree sinogram to a 360-sinogram.
-- Generating a sinogram from a helical data.
+    - Stitching images.
+    - Joining images if there is no overlapping.
+    - Converting a 360-degree sinogram with offset center-of-rotation (COR) to
+      a 180-degree sinogram.
+    - Extending a 360-degree sinogram with offset COR for direct reconstruction
+      instead of converting it to a 180-degree sinogram.
+    - Converting a 180-degree sinogram to a 360-sinogram.
+    - Generating a sinogram from a helical data.
 """
 
 import numpy as np

algotom/prep/correction.py

@@ -22,12 +22,12 @@
 
 """
 Module of correction methods in the preprocessing stage:
-- Flat-field correction.
-- Distortion correction.
-- MTF deconvolution.
-- Tilted sinogram generation.
-- Tilted 1D intensity-profile generation.
-- Beam hardening correction.
+    - Flat-field correction.
+    - Distortion correction.
+    - MTF deconvolution.
+    - Tilted sinogram generation.
+    - Tilted 1D intensity-profile generation.
+    - Beam hardening correction.
 """
 
 import numpy as np
@@ -60,8 +60,8 @@ def flat_field_correction(proj, flat, dark, ratio=1.0, use_dark=True,
     options : dict, optional
         Apply a zinger removal method and/or ring removal methods.
         E.g option1={"method": "dezinger", "para1": 0.001, "para2": 1},
-        option2={"method": "remove_stripe_based_sorting",
-                "para1": 15, "para2": 1}
+        option2={"method": "remove_stripe_based_sorting", "para1": 15,
+        "para2": 1}
 
     Returns
     -------

algotom/prep/filtering.py

@@ -22,8 +22,8 @@
 
 """
 Module of filtering methods in the preprocessing stage:
-- Fresnel filter (denoising or low-pass filter).
-- Double-wedge filter.
+    - Fresnel filter (denoising or low-pass filter).
+    - Double-wedge filter.
 """
 
 import numpy as np

algotom/prep/removal.py

@@ -22,10 +22,10 @@
 
 """
 Module of removal methods in the preprocessing stage:
-- Many methods for removing stripe artifact in a sinogram (<-> ring artifact
-in a reconstructed image).
-- A zinger removal method.
-- Blob removal methods.
+    - Many methods for removing stripe artifact in a sinogram (<-> ring artifact
+      in a reconstructed image).
+    - A zinger removal method.
+    - Blob removal methods.
 """
 
 import numpy as np

algotom/rec/reconstruction.py

@@ -22,10 +22,10 @@
 
 """
 Module of FFT-based reconstruction methods in the reconstruction stage:
-- Filtered back-projection (FBP) method for GPU (using numba and cuda) and CPU.
-- Direct Fourier inversion (DFI) method.
-- Wrapper for Astra Toolbox reconstruction (optional)
-- Wrapper for Tomopy-gridrec reconstruction (optional)
+    - Filtered back-projection (FBP) method for GPU (using numba and cuda) and CPU.
+    - Direct Fourier inversion (DFI) method.
+    - Wrapper for Astra Toolbox reconstruction (optional)
+    - Wrapper for Tomopy-gridrec reconstruction (optional)
 """
 
 import math

algotom/util/calibration.py

@@ -22,10 +22,10 @@
 
 """
 Module of calibration methods:
-- Correcting the non-uniform background of an image.
-- Binarizing an image.
-- Calculating the distance between two point-like objects segmented from
-  two images. Useful for determining pixel-size in helical scans.
+    - Correcting the non-uniform background of an image.
+    - Binarizing an image.
+    - Calculating the distance between two point-like objects segmented from
+      two images. Useful for determining pixel-size in helical scans.
 """
 
 import numpy as np

algotom/util/config.py

@@ -1,19 +1,21 @@
+# ============================================================================
+# Author: Francesco De Carlo
+# Description: Configuration module
+# Contributors:
+# ============================================================================
+
 import os
 import sys
 import pathlib
 import argparse
 import configparser
-import numpy as np
 from collections import OrderedDict
 from pathlib import Path
-
 from algotom.util import log
 
-LOGS_HOME = Path.home()/'logs'
+LOGS_HOME = Path.home() / 'logs'
 CONFIG_FILE_NAME = os.path.join(str(pathlib.Path.home()), 'algotom.conf')
-
 SECTIONS = OrderedDict()
-
 SECTIONS['general'] = {
     'config': {
         'default': CONFIG_FILE_NAME,
@@ -39,13 +41,11 @@
         'type': str,
         'default': "D:/output/",
         'help': "string"},
-        }
-
-
-EXPLORE_PARAMS = ('explore', )
-
+}
+EXPLORE_PARAMS = ('explore',)
 NICE_NAMES = ('General', 'Explore')
 
+
 def get_config_name():
     """Get the command line --config option."""
     name = CONFIG_FILE_NAME
@@ -58,7 +58,6 @@ def get_config_name():
                 if name[0] == '=':
                     name = name[1:]
                 return name
-
     return name
 
 
@@ -72,10 +71,9 @@ def parse_known_args(parser, subparser=False):
         subparser_value = [sys.argv[1]] if subparser else []
         config_values = config_to_list(config_name=get_config_name())
         values = subparser_value + config_values + sys.argv[1:]
-        #print(subparser_value, config_values, values)
+        # print(subparser_value, config_values, values)
     else:
         values = ""
-
     return parser.parse_known_args(values)[0]
 
 
@@ -87,34 +85,30 @@ def config_to_list(config_name=CONFIG_FILE_NAME):
     """
     result = []
     config = configparser.ConfigParser()
-
     if not config.read([config_name]):
         return []
 
     for section in SECTIONS:
-        for name, opts in ((n, o) for n, o in SECTIONS[section].items() if config.has_option(section, n)):
+        for name, opts in ((n, o) for n, o in SECTIONS[section].items() if
+                           config.has_option(section, n)):
             value = config.get(section, name)
-
             if value != '' and value != 'None':
                 action = opts.get('action', None)
-
                 if action == 'store_true' and value == 'True':
                     # Only the key is on the command line for this action
                     result.append('--{}'.format(name))
-
                 if not action == 'store_true':
                     if opts.get('nargs', None) == '+':
                         result.append('--{}'.format(name))
                         result.extend((v.strip() for v in value.split(',')))
                     else:
                         result.append('--{}={}'.format(name, value))
-
     return result
 
 
 class Params(object):
     def __init__(self, sections=()):
-        self.sections = sections + ('general', )
+        self.sections = sections + ('general',)
 
     def add_parser_args(self, parser):
         for section in self.sections:
@@ -129,7 +123,6 @@ def add_arguments(self, parser):
     def get_defaults(self):
         parser = argparse.ArgumentParser()
         self.add_arguments(parser)
-
         return parser.parse_args('')
 
 
@@ -144,16 +137,15 @@ def write(config_file, args=None, sections=None):
     for section in SECTIONS:
         config.add_section(section)
         for name, opts in SECTIONS[section].items():
-            if args and sections and section in sections and hasattr(args, name.replace('-', '_')):
+            if (args and sections and section in sections) \
+                    and hasattr(args, name.replace('-', '_')):
                 value = getattr(args, name.replace('-', '_'))
                 if isinstance(value, list):
                     # print(type(value), value)
                     value = ', '.join(value)
             else:
                 value = opts['default'] if opts['default'] is not None else ''
-
             prefix = '# ' if value == '' else ''
-
             if name != 'config':
                 config.set(section, prefix + name, str(value))
     with open(config_file, 'w') as f:
@@ -187,11 +179,11 @@ def show_config(args):
 
     log.warning('algotom status start')
     for section, name in zip(SECTIONS, NICE_NAMES):
-        entries = sorted((k for k in args.keys() if k.replace('_', '-') in SECTIONS[section]))
+        entries = sorted((k for k in args.keys() if
+                          k.replace('_', '-') in SECTIONS[section]))
         if entries:
             for entry in entries:
                 value = args[entry] if args[entry] != None else "-"
                 log.info("  {:<16} {}".format(entry, value))
 
     log.warning('algotom status end')
-

algotom/util/log.py

@@ -1,6 +1,5 @@
 '''
-    tomoscan custom logger
-    
+Logger
 '''
 import logging
 
@@ -24,7 +23,8 @@ def setup_custom_logger(lfname=None, stream_to_console=True):
 
     if (lfname != None):
         fHandler = logging.FileHandler(lfname)
-        file_formatter = logging.Formatter('%(asctime)s - %(levelname)s: %(message)s')
+        file_formatter = logging.Formatter('%(asctime)s - %(levelname)s:'
+                                           ' %(message)s')
         fHandler.setFormatter(file_formatter)
         logger.addHandler(fHandler)
     if stream_to_console:

algotom/util/simulation.py

@@ -23,10 +23,10 @@
 
 """
 Module of simulation methods:
-1- Methods for designing a customized 2D phantom.
-2- Method for calculating a sinogram of a phantom based on the Fourier
-   slice theorem.
-3- Methods for adding artifacts to a simulated sinogram.
+    - Methods for designing a customized 2D phantom.
+    - Method for calculating a sinogram of a phantom based on the Fourier
+      slice theorem.
+    - Methods for adding artifacts to a simulated sinogram.
 """
 
 import numpy as np