Merge pull request #202 from pydicom/add/new-ctp-rules

updating or adding new ctp rules
pydicom · Mar 23, 2022 · 2718b7e · 2718b7e
2 parents a0c630e + d0fcfc7
commit 2718b7e
Show file tree

Hide file tree

Showing 44 changed files with 135 additions and 60 deletions.
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -1,5 +1,4 @@
----
-name: Codespell
+name: Check for Typos
 
 on:
   push:
@@ -15,3 +14,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: codespell-project/actions-codespell@de089481bd65b71b4d02e34ffb3566b6d189333e
+        uses: crate-ci/typos@592b36d23c62cb378f6097a292bc902ee73f93ef # version 1.0.4
+        with: 
+          files: ./deid ./docs/_docs ./docs/README.md ./docs/pages ./examples
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,7 +14,8 @@ and **Merged pull requests**. Critical items to know are:
 Referenced versions in headers are tagged on Github, in parentheses are for pypi.
 
 ## [vxx](https://github.com/pydicom/deid/tree/master) (master)
- - various LGTM alert fixes [#186](https://github.com/pydicom/deid/pull/186)
+ - update CTP deid.dicom up until [this commit](https://github.com/johnperry/CTP/commit/345b05b157c046532e8791a63ababbf6d0dba59b) (0.2.29)
+ - various LGTM alert fixes [#186](https://github.com/pydicom/deid/pull/186) (0.0.28)
  - bug fix for exception when attempting to jitter DA/DT which cannot be jittered (space) [#189] (https://github.com/pydicom/deid/issues/189) (0.2.27)
  - adding support to manipulate file meta [#183](https://github.com/pydicom/deid/issues/183) (0.2.26)
  - updated pydicom dependency from 1.3.0 to 2.1.1 [#171](https://github.com/pydicom/deid/issues/171) (0.2.25)

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,4 @@
-MIT License
-
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/config/__init__.py b/deid/config/__init__.py
@@ -2,7 +2,7 @@
 
 DeidRecipe
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -32,8 +32,6 @@
 from deid.config.standards import actions, sections, formats
 
 from deid.logger import bot
-import os
-import re
 
 
 class DeidRecipe:

diff --git a/deid/config/standards.py b/deid/config/standards.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/config/utils.py b/deid/config/utils.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/data/__init__.py b/deid/data/__init__.py
@@ -4,7 +4,7 @@
 
    from deid.data import get_dataset
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/data/deid.dicom b/deid/data/deid.dicom
@@ -161,6 +161,36 @@ LABEL Overlay # (CTP)
   + contains OverlayDescription Siemens MedCom Object Graphics
   coordinates 0,0,512,90
 
+
+LABEL Philips PT # (CTP)
+  contains Modality PT
+  + contains Manufacturer Philips
+  + contains ManufacturerModelName GEMINI
+  + equals Rows 446
+  + equals Columns 245
+  coordinates 0,0,125,50
+
+LABEL Philips PT # (CTP)
+  contains Modality PT
+  + contains Manufacturer Philips
+  + contains ManufacturerModelName GEMINI
+  + equals Rows 445
+  + equals Columns 493
+  coordinates 0,0,140,55
+
+LABEL Philips PT # (CTP)
+  contains Modality PT
+  + contains Manufacturer Philips
+  + contains ManufacturerModelName GEMINI
+  + equals Rows 373
+  + equals Columns 492
+  coordinates 0,0,100,25
+
+LABEL MINDRAY # (CTP)
+  contains Modality US
+  + contains ImplementationVersionName MINDRAY
+  coordinates 0,0,1229,69
+
 LABEL Logiq US (LOGIQ9) # (CTP)
   contains Modality US
   + contains Manufacturer GE
@@ -227,14 +257,14 @@ LABEL EPIQ 7G # (CTP)
   + contains Manufacturer Philips
   + equals Rows 600
   + contains ManufacturerModelName EPIQ
-  coordinates 0,0,800,59
+  coordinates 0,0,1024,49
 
 LABEL EPIQ 7G # (CTP)
   contains Modality US
   + contains Manufacturer Philips
   + equals Rows 768
   + contains ManufacturerModelName EPIQ
-  coordinates 0,0,800,59
+  coordinates 0,0,1024,49
 
 LABEL EPIQ 7G # (FFUR)
   contains Modality US
@@ -249,6 +279,11 @@ LABEL CX50 # (CTP)
   + contains ManufacturerModelName CX50
   coordinates 0,0,800,59
 
+LABEL EPIQ_7G (CTP)
+  + contains Manufacturer EPIQ
+  + equals Rows 600|768
+  coordinates 0,0,800,59
+
 LABEL Z_ONE # (CTP)
   contains Modality US 
   + contains Manufacturer Zonare
@@ -352,7 +387,7 @@ LABEL Acuson Sequoia # (CTP)
   + contains ManufacturerModelName SEQUOIA
   coordinates 0,0,640,30
 
-LABEL Aplio 400 or 500 # (CTP)
+LABEL Toshiba Aplio 400 or 500 # (CTP)
   contains Modality US
   + contains Manufacturer TOSHIBA
   + equals Rows 720
@@ -396,6 +431,20 @@ LABEL Supersonic Imagine 5A # (CTP)
   + contains ManufacturerModelName Aixplorer
   coordinates 0,0,1400,89
 
+LABEL SENO # (CTP)
+  contains Modality US
+  + contains Manufacturer SENO
+  + equals Rows 1058
+  + equals Columns 1920
+  coordinates 161,0,1632,50
+
+LABEL SENO Cine # (CTP)
+  contains Modality US
+  + contains Manufacturer SENO
+  + equals Rows 1056
+  + equals Columns 1920
+  coordinates 161,0,1632,50
+
 LABEL Canon CR/DR # (CTP)
   contains Modality MRI
   + contains Manufacturer Canon
@@ -410,17 +459,44 @@ LABEL Siemens NM # (CTP)
   + equals Rows 860
   + contains ManufacturerModelName CXD1
   + contains ImageType SECONDARY
-  coordinates 0,0,1132,82
+  coordinates 0,0,1132,90
+  coordinates 0,780,1132,80
+
+LABEL Siemens NM # (CTP)
+  contains Modality NM
+  + contains Manufacturer Siemens
+  + equals Rows 860
+  + contains ImageType SECONDARY
+  coordinates 0,0,1132,90
   coordinates 0,780,1132,80
 
+LABEL Siemens NM # (CTP)
+  contains Modality NM
+  + contains Manufacturer Siemens
+  + equals Rows 865
+  + contains ImageType SECONDARY
+  coordinates 0,0,1132,35
+
+LABEL Siemens NM # (CTP)
+  contains Modality NM
+  + contains Manufacturer Siemens
+  + equals Rows 882
+  + contains ImageType SECONDARY
+  coordinates 0,0,1132,65
+
+LABEL ADAC # (CTP)
+  equals Rows 832
+  + equals Columns 1024
+  + contains Manfacturer ADAC
+  coordinates 0,0,1024,80
+  coordinates 0,762,1024,80
 
 LABEL ADAC # (CTP)
-  contains Modality Other
-  + contains Manufacturer ADAC
-  + equals Rows 832
+  equals Rows 832
   + equals Columns 1024
   + contains Manfacturer ADAC
-  coordinates 0,0,1024,60
+  + contains ProtocolName DUAL DETEC
+  coordinates 0,0,1024,130
   coordinates 0,762,1024,80
 
 LABEL MEDRAD Injection Profile # (CTP)

diff --git a/deid/dicom/actions.py b/deid/dicom/actions.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/fields.py b/deid/dicom/fields.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/filter.py b/deid/dicom/filter.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/groups.py b/deid/dicom/groups.py
@@ -2,7 +2,7 @@
 
 groups: functions to derive groups of fields or values
 
-Copyright (c) 2020-2021 Vanessa Sochat
+Copyright (c) 2020-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/header.py b/deid/dicom/header.py
@@ -2,7 +2,7 @@
 
 header.py: functions to extract identifiers from dicom headers
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/parser.py b/deid/dicom/parser.py
@@ -2,7 +2,7 @@
 
 parser.py: class that supports dicom extraction and replacement of fields.
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -344,7 +344,7 @@ def perform_action(self, field, value, action, filemeta=False):
             values = self.lookup.get(re.sub("^values:", "", field), [])
             fields = self.find_by_values(values=values)
 
-        # A fields list is used vertabim
+        # A fields list is used vertbatim
         # In expand_field_expression below, the stripped_tag is being passed in to field.  At this point,
         # expanders for %fields lists have already been processed and each of the contenders is an
         # identified, unique field.  It is important to use stripped_tag at this point instead of

diff --git a/deid/dicom/pixels/clean.py b/deid/dicom/pixels/clean.py
@@ -2,7 +2,7 @@
 
 clean.py: functions for pixel scrubbing
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -322,7 +322,7 @@ def save_animation(self, output_folder=None, image_type="cleaned", title=None):
         enough frames, then save_png should be used instead.
         """
         if hasattr(self, image_type):
-            from matplotlib import animation, rc
+            from matplotlib import animation
 
             animation.rcParams["animation.writer"] = "ffmpeg"
 

diff --git a/deid/dicom/pixels/detect.py b/deid/dicom/pixels/detect.py
@@ -2,7 +2,7 @@
 
 detect.py: functions for pixel scrubbing
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/tags.py b/deid/dicom/tags.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/utils.py b/deid/dicom/utils.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/dicom/validate.py b/deid/dicom/validate.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/logger/message.py b/deid/logger/message.py
@@ -2,7 +2,7 @@
 
 logger/message.py: Python logger base
 
-Copyright (c) 2016-2021 Vanessa Sochat
+Copyright (c) 2016-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/main/__init__.py b/deid/main/__init__.py
@@ -2,7 +2,7 @@
 
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/main/identifiers.py b/deid/main/identifiers.py
@@ -2,7 +2,7 @@
 
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/main/inspect.py b/deid/main/inspect.py
@@ -2,7 +2,7 @@
 
 """
 
-Copyright (c) 2017-2021 Vanessa Sochat
+Copyright (c) 2017-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/tests/Xtest_dicom_header.py b/deid/tests/Xtest_dicom_header.py
@@ -5,7 +5,7 @@
 
 The MIT License (MIT)
 
-Copyright (c) 2016-2021 Vanessa Sochat
+Copyright (c) 2016-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/tests/common.py b/deid/tests/common.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 """
-Copyright (c) 2016-2021 Vanessa Sochat
+Copyright (c) 2016-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/deid/tests/test_clean.py b/deid/tests/test_clean.py
@@ -3,7 +3,7 @@
 """
 Test DICOM Cleaner
 
-Copyright (c) 2016-2021 Vanessa Sochat
+Copyright (c) 2016-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal