Typos found by codespell (#185)

README.md

@@ -5,7 +5,7 @@ Best effort anonymization for medical images in Python.
 [![DOI](https://zenodo.org/badge/94163984.svg)](https://zenodo.org/badge/latestdoi/94163984)
 [![Build Status](https://travis-ci.org/pydicom/deid.svg?branch=master)](https://travis-ci.org/pydicom/deid)
 
-Please see our [Documentation](https://pydicom.github.io/deid/)
+Please see our [Documentation](https://pydicom.github.io/deid/).
 
 These are basic Python based tools for working with medical images and text, specifically for de-identification.
 The cleaning method used here mirrors the one by CTP in that we can identify images based on known
@@ -35,4 +35,4 @@ docker run pydicom/deid --help
 ```
 
 ## Issues
-If you have an issue, or want to request a feature, please do so on our [issues board](https://www.github.com/pydicom/deid/issues)
+If you have an issue, or want to request a feature, please do so on our [issues board](https://www.github.com/pydicom/deid/issues).

deid/config/__init__.py

@@ -177,7 +177,7 @@ def ls_fieldlists(self):
     # Init
 
     def _init_deid(self, deid=None, base=False, default_base="dicom"):
-        """initalize the recipe with one or more deids, optionally including
+        """initialize the recipe with one or more deids, optionally including
         the default. This function is called at init time. If you need to add
         or work with already loaded configurations, use add/remove
 

deid/config/utils.py

@@ -289,7 +289,7 @@ def parse_label(section, config, section_name, members, label=None):
     section: the section name (e.g., header) must be one in sections
     config: the config (dictionary) parsed thus far
     section_name: an optional name for a section
-    members: the lines beloning to the section/section_name
+    members: the lines belonging to the section/section_name
     label: an optional name for the group of commands
     """
     criteria = {"filters": [], "coordinates": []}

deid/data/README.md

@@ -30,4 +30,3 @@ def get_dicom(dataset):
 
 dicom = get_dicom(dataset)
 ```
-

deid/dicom/groups.py

@@ -75,7 +75,7 @@ def extract_values_list(dicom, actions, fields=None):
                     param_name = param_name.strip()
                     param_val = param_val.strip()
 
-                    # Set a custom parameter legnth
+                    # Set a custom parameter length
                     if param_name == "minlength":
                         minlength = int(param_val)
                         bot.debug("Minimum length set to %s" % minlength)

deid/dicom/parser.py

@@ -402,7 +402,7 @@ def update_dicom(element, is_filemeta):
         # Assume we don't want to add an empty value
         if value is not None:
 
-            # If provided a field object, create based on keyword or tag identifer
+            # If provided a field object, create based on keyword or tag identifier
             name = field
             if isinstance(field, DicomField):
                 name = field.element.keyword or field.stripped_tag

deid/dicom/pixels/clean.py

@@ -243,7 +243,7 @@ def clean(self, fix_interpretation=True, pixel_data_attribute="PixelData"):
                 # apply final 3D mask to 3D pixel data
                 self.cleaned = final_mask * self.original
 
-            # greyscale image: no need to stack into the channel dim since it doesnt exist
+            # greyscale image: no need to stack into the channel dim since it doesn't exist
             elif len(self.original.shape) == 2:
                 self.cleaned = mask * self.original
 

deid/utils/actions.py

@@ -84,7 +84,7 @@ def get_func(function_name):
 
 def get_timestamp(item_date, item_time=None, jitter_days=None, format=None):
     """get_timestamp will return (default) a UTC timestamp
-    with some date and (optionall) time. A different format can be
+    with some date and (optional) time. A different format can be
     provided to change default behavior. eg: "%Y%m%d"
     """
     if format is None:

docs/_docs/development/image-format.md

@@ -18,13 +18,13 @@ deid
 This folder, and others like it, should contain should contain the following files:
 
  - **config.json** this is the default specification for how a dicom header is parsed, which primarily means additions, and a set of custom actions. 
- - **__init__.py**: has the purpose of exposing module functions to the higher up folder for import. For example, the function `get_identifiers` in [header.py](header.py) is programatically accessible via `from deid.dicom import get_identifiers` thanks to this file. If you create a new module with the equivalent functions, you should be fine to just copy this file, or import the functions directly from tasks.py in the module folder.
+ - **__init__.py**: has the purpose of exposing module functions to the higher up folder for import. For example, the function `get_identifiers` in [header.py](header.py) is programmatically accessible via `from deid.dicom import get_identifiers` thanks to this file. If you create a new module with the equivalent functions, you should be fine to just copy this file, or import the functions directly from tasks.py in the module folder.
  - **header.py**: should contain functions for `get_identifiers`, which should return a dictionary with top level indexes by entity, and the value of each entity another dictionary indexed by the item ids. This data structure, if provided by the client, must be understood by the function `remove_identifiers`.
 
 Note that, since we are working in Python, we will be using dicom headers 
 that are mapped from the standard to pydicom, the entire mapping which is 
 provided [here](https://github.com/pydicom/pydicom/blob/master/pydicom/_dicom_dict.py), 
-and programatically accessible via:
+and programmatically accessible via:
 
 ```python
 from pydicom._dicom_dict import DicomDictionary

docs/_docs/examples/recipe.md

@@ -58,7 +58,7 @@ recipe.get_format()
 ```
 
 Note that validation of this structure happens at load time. If something is 
-incorrecly labeled or formatted, you will get an error message and it will 
+incorrectly labeled or formatted, you will get an error message and it will 
 fail to load. You can also provide your own deid recipe file, and in 
 doing so, you won't load the default. Here is one from our examples folder
 

docs/_docs/getting-started/dicom-pixels.md

@@ -141,7 +141,7 @@ By default, we use a list of rules provided by CTP and other users in [dicom.dei
 There are two operations we can apply to coordinates:
 
  - `keepcoordinates` indicates a set of coordinates that you want to set the mask to a value of 1, to indicate keeping
- - `coordinates` indicates a set of coordintes that you want to set the mask to a value of 0, to indicate cleaning.
+ - `coordinates` indicates a set of coordinates that you want to set the mask to a value of 0, to indicate cleaning.
 
 By default, deid will start with a mask of all 1s, indicating that we keep all coordinates. We then
 apply the list of rules provided by CTP and others in [dicom.deid](https://github.com/pydicom/deid/blob/master/deid/data/deid.dicom)
@@ -341,4 +341,3 @@ client.clean(fix_interpretation=False)
 Please [see the note](https://pydicom.github.io/pydicom/stable/old/image_data_handlers.html#usage)
 on the pydicom documentation for more details. Also, it would be useful to use machine 
 learning to detect text. if you want to develop this or have ideas, please reach out.
-

docs/_docs/getting-started/dicom-put.md

@@ -300,7 +300,7 @@ cleaned_dicoms = replace_identifiers(dicom_files=dicom_files)
 ```
 
 The default recipe you can view [here](https://github.com/pydicom/deid/blob/master/deid/data/deid.dicom#L744).
-It's fairly agressive and generally removes times and other identifiers. But *you should not use this verbatim!*
+It's fairly aggressive and generally removes times and other identifiers. But *you should not use this verbatim!*
 It's important that you develop a strategy that is most robust for your datasets.
 The example is provided as a conservative start. If you want to save to temporary
 files, you can specify save=True:

docs/_docs/user-docs/index.md

@@ -23,6 +23,3 @@ these pages will help you to use the deid software.
 ## Tools
 
  - [Tags]({{ site.baseurl }}/user-docs/tags): A few helpful functions for searching and filtering tags.
-
-
-

examples/deid/README.md

@@ -2,5 +2,5 @@
 
 This is a folder of deid recipe examples. If you have a recipe that you think
 would be useful for others, please contribute it here! You can also
-add it to be included with the library (under ded/data) if you think this
+add it to be included with the library (under deid/data) if you think this
 level of contribution is more relevant.

examples/dicom/pixels/run-cleaner-client.py

@@ -26,7 +26,7 @@
 
 client = DicomCleaner()
 
-# You can set the output folder if you want, otherwis tmpdir is used
+# You can set the output folder if you want, otherwise tmpdir is used
 client = DicomCleaner(output_folder="/home/vanessa/Desktop")
 
 # Steps are to detect, clean, and save in desired format, one image