Dbodor/prospector fixes

cvasl/carve.py

@@ -17,17 +17,12 @@
 from abc import ABC, abstractmethod
 
 
-from datetime import datetime, date
+from datetime import date
 
 import pandas as pd
 import SimpleITK as sitk
 
-import numpy
-from datetime import datetime, date
 import pydicom as dicom
-import pandas as pd
-import skimage.io as io
-
 from pydicom.multival import MultiValue
 from pydicom.sequence import Sequence
 
@@ -118,10 +113,10 @@ def get_tag(self):
         return self.tag
 
     def items(self, reader, transformer=None):
-        for file in glob(self.exp, recursive=self.recursive):
+        for file in glob(self.exp, recursive=self.recursive):  #TODO: glob is not callable, what are we trying to loop over here
             parsed = reader(file)
             if transformer is not None:
-                full_path = transformer(file)
+                self.full_path = transformer(file)
             yield file, parsed
 
 
@@ -143,7 +138,7 @@ def items(self, reader, transformer=None):
 def rename_file(original, target, ext):
     dst_file = os.path.basename(original)
     dst_file = os.path.splitext(dst_file)[0]
-    return os.path.join(target, '{}.{}'.format(dst_file, ext))
+    return os.path.join(target, f'{dst_file}.{ext}')
 
 
 class PydicomDicomReader:
@@ -205,6 +200,8 @@ def __init__(
             self.exclude_field_types = exclude_field_types
         if date_fields:
             self.date_fields = date_fields
+        if time_fields:
+            self.time_fields = time_fields
         if exclude_fields:
             self.exclude_fields = exclude_fields
 
@@ -263,12 +260,6 @@ def read(self, source):
         return pd.DataFrame(columns)
 
 
-def rename_file(original, target, ext):
-    dst_file = os.path.basename(original)
-    dst_file = os.path.splitext(dst_file)[0]
-    return os.path.join(target, '{}.{}'.format(dst_file, ext))
-
-
 tag_dictionary = {   # 'key' , 'datapoint_name'
     '0002|0000': 'File Meta Information Group Length',
     '0002|0001': 'File Meta Information Version',
@@ -438,7 +429,7 @@ def fetch_image(self, dicom_file):
         # not a file name.
         self.reader.SetFileName(dicom_file)
         dcm = self.reader.Execute()
-        return sitk.GetArrayFromImage(image)
+        return sitk.GetArrayFromImage(dcm)  #TODO check that dcm is correct parameter instead of `image`
 
 
 class SimpleITKDicomReader:
@@ -567,9 +558,9 @@ def rip_out_array_sitk(dicomfile_directory):
     dicom_files = glob.glob(dicomfile_directory + '/*')
     reader = sitk.ImageFileReader()
     saved_images = []
-    for i in range(len(dicom_files)):
+    for file in dicom_files:
         # give the reader a filename
-        reader.SetFileName(dicom_files[i])
+        reader.SetFileName(file)
         # use the reader to read the image
         image = reader.Execute()
         image_np = sitk.GetArrayFromImage(image)

cvasl/cli.py

@@ -110,7 +110,7 @@ def make_parser():
     return parser
 
 
-def main(argv):
+def main(argv):  #pylint: disable=unused-argument
     """
     This runs the parser and subparsers.
     """

cvasl/file_handler.py

@@ -18,12 +18,7 @@
 import textwrap
 import hashlib
 import glob
-import math
 import pandas as pd
-import numpy as np
-import scipy
-from scipy import signal
-import random
 
 
 class Config:
@@ -110,13 +105,13 @@ def load(self, location):
         found = None
         for p in locations:
             try:
-                with open(p) as f:
+                with open(p, encoding="utf-8") as f:
                     self._raw = json.load(f)
                     found = p
                     break
             except json.JSONDecodeError as e:
                 raise ValueError(
-                    'Cannot parse configuration in {}'.format(p),
+                    f'Cannot parse configuration in {p}',
                 ) from e
             except Exception as e:
                 logging.info('Configuration not found in %s: %s', p, e)
@@ -128,11 +123,10 @@ def load(self, location):
         if root is None:
             required = dict(self.default_layout)
             del required['bids']
-            for directory in required.keys():
+            for directory in required:
                 if directory not in self._raw:
                     raise ValueError(
-                        'Configuration in {} is missing required directory {}'
-                        .format(found, directory),
+                        f'Configuration in {found} is missing required directory {directory}',
                     )
             # User specified all concrete directories.  Nothing for us to
             # do here.
@@ -150,10 +144,8 @@ def validate(self):
         for d in self.required_directories:
             if not os.path.isdir(self._loaded[d]):
                 raise ValueError(
-                    'Required directory {}: {} doesn\'t exist'.format(
-                        d,
-                        self._loaded[d],
-                    ))
+                    f'Required directory {d}: {self._loaded[d]} does not exist'
+                    )
 
     def get_directory(self, directory, value=None):
         if value is None:

cvasl/mold.py

@@ -10,7 +10,6 @@
 import os
 import glob
 import numpy as np
-from ipywidgets import IntSlider, Output
 import ipywidgets as widgets
 import matplotlib.pyplot as plt
 
@@ -109,7 +108,7 @@ def plot_slice(self, z):
 
 def n4_debias_sitk(
         image_filename,
-        iteration_vector=[20, 10, 10, 5],
+        iteration_vector=None,
         masking=True
 ):
     """
@@ -119,6 +118,10 @@ def n4_debias_sitk(
     Need to cite SITK
     """
     # TODO: add sitk citation in docstring,
+
+    if iteration_vector is None:
+        iteration_vector = [20, 10, 10, 5]
+
     inputImage = sitk.ReadImage(image_filename)
     bits_in_input = inputImage.GetPixelIDTypeAsString()
     bit_dictionary = {"Signed 8 bit integer": sitk.sitkInt8,
@@ -191,7 +194,7 @@ def debias_folder(file_directory, algorithm, processed, force=False):
         if algorithm == 'n4_debias_sitk':
             array = n4_debias_sitk(file)
         elif algorithm == 'alternative_debias_a':
-            array = alternative_debias_a(file)
+            array = alternative_debias_a(file)  #TODO: what is this?
 
         else:
             array = n4_debias_sitk(file)

cvasl/seperated.py

@@ -12,7 +12,6 @@
 import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
-import copy
 import glob
 import os
 
@@ -83,11 +82,11 @@ def relate_columns_graphs(dataframe, special_column_name):
     a = len(col)  # number of rows
     b = 1  # number of columns
     c = 1  # initialize plot counter
-    fig = plt.figure(figsize=(10, (len(col)*10)))
+    fig = plt.figure(figsize=(10, (len(col)*10)))  # noqa=F841, pylint: disable=unused-variable
     for i in col:
         plt.subplot(a, b, c)
         plt.scatter(dataframe[i].apply(pd.to_numeric), y)
-        plt.title('{}, subplot: {}{}{}'.format(i, a, b, c))
+        plt.title(f'{i}, subplot: {a}{b}{c}')
         plt.xlabel(i)
         c = c + 1
     plt.savefig(("versus" + special_column_name + ".png"))
@@ -155,8 +154,7 @@ def generate_transformation_matrix(polynomial1, polynomial2):
     for i, (c1, c2) in enumerate(zip(polynomial1, polynomial2)):
         m[i][i] = c2/c1
 
-    return m
-
+    return m 
 
 
 def find_original_y_values(polynomial, output_value):

environment.yml

@@ -16,13 +16,13 @@ dependencies:
   - numexpr=2.7.3
   - numpy=1.22.3
   - pandas
+  - pydicom
   - pycodestyle
   - scipy=1.7.3
   - scikit-image=0.19.2
   - seaborn
   - simpleitk=2.2.1
   - sphinx=4.5.0
-  - pydicom