Small nitpicks

NeuroRuler/utils/global_vars.py

@@ -2,22 +2,24 @@
 
 import SimpleITK as sitk
 from pathlib import Path
-from typing import Any
 from NeuroRuler.utils.constants import View
 
 IMAGE_DICT: dict[Path, sitk.Image] = dict()
-"""The group of images that have been loaded.
+"""The group of images that has been loaded.
 
-Since Python 3.7+, dicts maintain insertion order. Therefore, we can use CURR_IMAGE_INDEX for retrieval and deletion.
+Since Python 3.7+, dicts maintain insertion order. Therefore, we can use
+CURR_IMAGE_INDEX for retrieval and deletion.
 
 Use list(IMAGE_DICT.keys())[i] to return the i'th key in the dict, which can also index into the dict.
 Not sure about this operation's speed, but it's used only
-in the GUI for insertion and deletion operations, should be fine.
+in the GUI for insertion and deletion operations, which is fine.
 
-All images in the dictionary have matching properties, as defined by mri_image.get_properties."""
+All images in the dictionary have matching properties, as defined by img_helpers.ImageProperties
+(there is a threshold for pixel spacing)."""
 
 GROUP_MAX_SPACING_DIFF: float = 0.0001
-"""The maximum difference in pixel spacing (in mm) between two images of the global group, such that they may be considered to be the same spacing."""
+"""The maximum difference in pixel spacing (in mm) between two images of the global group,
+such that they are considered to have the same spacing."""
 
 CURR_IMAGE_INDEX: int = 0
 """Image of the current image in the loaded batch of images, which is a dict[Path, sitk.Image].
@@ -29,7 +31,7 @@
 """Global ``sitk.ImageFileReader``."""
 
 ORIENT_FILTER: sitk.DICOMOrientImageFilter = sitk.DICOMOrientImageFilter()
-"""Global sitk.DICOMOrientImageFilter for orienting images.
+"""Global ``sitk.DICOMOrientImageFilter`` for orienting images.
 
 See https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1DICOMOrientImageFilter.html#details
 and the orientation strings in constants.py. Use ITK-SNAP for the orientations that we copy."""

NeuroRuler/utils/gui_settings.py

@@ -8,7 +8,6 @@
 then we need an actual working value here."""
 
 from pathlib import Path
-import NeuroRuler.utils.constants as constants
 
 DEBUG: bool = False
 """Whether or not to print debugging information throughout execution."""
@@ -40,4 +39,5 @@
 """Whether the advanced menu messages display in terminal or new window"""
 
 GROUP_MAX_SPACING_DIFF: float = 0.0001
-"""The maximum difference in pixel spacing (in mm) between two images of the global group, such that they may be considered to be the same spacing. See global_vars.GROUP_MAX_SPACING_DIFF."""
+"""The maximum difference in pixel spacing (in mm) between two images of the global group,
+such that they are considered to have the same spacing. See ``global_vars.GROUP_MAX_SPACING_DIFF``."""

NeuroRuler/utils/img_helpers.py

@@ -9,6 +9,12 @@
 import NeuroRuler.utils.constants as constants
 
 
+class ImageProperties(NamedTuple):
+    center: tuple
+    size: tuple
+    spacing: tuple
+
+
 def update_images(path_list: list[Path]) -> list[Path]:
     """Initialize IMAGE_DICT. See the docstring for IMAGE_DICT in global_vars.py for more info.
 
@@ -147,20 +153,14 @@ def get_curr_image() -> sitk.Image:
     return global_vars.IMAGE_DICT[get_curr_path()]
 
 
-class ImageProperties(NamedTuple):
-    center: tuple
-    size: tuple
-    spacing: tuple
-
-
 # TODO: Add more properties?
 def get_properties_from_sitk_image(img: sitk.Image) -> ImageProperties:
     """Tuple of properties of a sitk.Image.
 
     TODO: Add more properties
 
-    If modifying this, NeuroRuler/GUI/main.py print_properties also has to be modified slightly,
-    as well are_properties_eq below.
+    If modifying this, NeuroRuler/GUI/main.py ``print_properties`` also has to be modified slightly,
+    as well as ``are_properties_eq`` below.
 
     :param img:
     :type img: sitk.Image
@@ -178,13 +178,17 @@ def are_properties_eq(props1: ImageProperties, props2: ImageProperties) -> bool:
     :type props1: ImageProperties
     :param props2:
     :type props2: ImageProperties
-    :return: true if the two image properties are considered equal.
+    :return: True if the two image properties are considered equal.
     :rtype: bool"""
     is_center_eq = props1.center == props2.center
     is_size_eq = props1.size == props2.size
     spacing1 = props1.spacing
     spacing2 = props2.spacing
-    is_spacing_eq = abs(spacing1[0] - spacing2[0]) <= global_vars.GROUP_MAX_SPACING_DIFF and abs(spacing1[1] - spacing2[1]) <= global_vars.GROUP_MAX_SPACING_DIFF and abs(spacing1[2] - spacing2[2]) <= global_vars.GROUP_MAX_SPACING_DIFF
+    is_spacing_eq = (
+        abs(spacing1[0] - spacing2[0]) <= global_vars.GROUP_MAX_SPACING_DIFF
+        and abs(spacing1[1] - spacing2[1]) <= global_vars.GROUP_MAX_SPACING_DIFF
+        and abs(spacing1[2] - spacing2[2]) <= global_vars.GROUP_MAX_SPACING_DIFF
+    )
 
     return is_center_eq and is_size_eq and is_spacing_eq
 

README.md

@@ -83,7 +83,7 @@ gui()
 python cli.py <file>
 ```
 
-See [test_cli.py](https://github.com/NIRALUser/NeuroRuler/blob/main/tests/test_cli.py) for example usages.
+See [test_cli.py](https://github.com/NIRALUser/NeuroRuler/blob/main/tests/test_cli.py) for example usages. Note that the CLI script accepts only one file at a time because it's expected that you'll use a shell script to loop over multiple files.
 
 ```text
 usage: cli.py [-h] [-d] [-r] [-x X] [-y Y] [-z Z] [-s SLICE] [-c CONDUCTANCE] [-i ITERATIONS] [-t STEP] [-f FILTER] [-l LOWER]

gui_config.json

@@ -20,7 +20,10 @@
     "STARTUP_WIDTH_RATIO": 0.75,
     "STARTUP_HEIGHT_RATIO": 0.7,
     "DISPLAY_ADVANCED_MENU_MESSAGES_IN_TERMINAL": "False",
-    // The maximum difference in pixel spacing (in mm) between two images of the global group, such that they may be considered to be the same spacing.
-    // If for some reason you don't want any tolerance, set this to 0.0.
+    // The maximum difference in pixel spacing (in mm) between any two images of the global group,
+    // such that they are considered to have the same spacing.
+    // For example, if pixel spacing is 0.0001, then the x spacing values of the two images have to be
+    // within 0.0001 of each other, and same for the y and z spacing values.
+    // If, for some reason, you don't want any tolerance, set this to 0.0.
     "GROUP_MAX_SPACING_DIFF": 0.0001
 }