brkraw 0.3.11__py3-none-any.whl → 0.5.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- brkraw/__init__.py +9 -3
- brkraw/apps/__init__.py +12 -0
- brkraw/apps/addon/__init__.py +30 -0
- brkraw/apps/addon/core.py +35 -0
- brkraw/apps/addon/dependencies.py +402 -0
- brkraw/apps/addon/installation.py +500 -0
- brkraw/apps/addon/io.py +21 -0
- brkraw/apps/hook/__init__.py +25 -0
- brkraw/apps/hook/core.py +636 -0
- brkraw/apps/loader/__init__.py +10 -0
- brkraw/apps/loader/core.py +622 -0
- brkraw/apps/loader/formatter.py +288 -0
- brkraw/apps/loader/helper.py +797 -0
- brkraw/apps/loader/info/__init__.py +11 -0
- brkraw/apps/loader/info/scan.py +85 -0
- brkraw/apps/loader/info/scan.yaml +90 -0
- brkraw/apps/loader/info/study.py +69 -0
- brkraw/apps/loader/info/study.yaml +156 -0
- brkraw/apps/loader/info/transform.py +92 -0
- brkraw/apps/loader/types.py +220 -0
- brkraw/cli/__init__.py +5 -0
- brkraw/cli/commands/__init__.py +2 -0
- brkraw/cli/commands/addon.py +327 -0
- brkraw/cli/commands/config.py +205 -0
- brkraw/cli/commands/convert.py +903 -0
- brkraw/cli/commands/hook.py +348 -0
- brkraw/cli/commands/info.py +74 -0
- brkraw/cli/commands/init.py +214 -0
- brkraw/cli/commands/params.py +106 -0
- brkraw/cli/commands/prune.py +288 -0
- brkraw/cli/commands/session.py +371 -0
- brkraw/cli/hook_args.py +80 -0
- brkraw/cli/main.py +83 -0
- brkraw/cli/utils.py +60 -0
- brkraw/core/__init__.py +13 -0
- brkraw/core/config.py +380 -0
- brkraw/core/entrypoints.py +25 -0
- brkraw/core/formatter.py +367 -0
- brkraw/core/fs.py +495 -0
- brkraw/core/jcamp.py +600 -0
- brkraw/core/layout.py +451 -0
- brkraw/core/parameters.py +781 -0
- brkraw/core/zip.py +1121 -0
- brkraw/dataclasses/__init__.py +14 -0
- brkraw/dataclasses/node.py +139 -0
- brkraw/dataclasses/reco.py +33 -0
- brkraw/dataclasses/scan.py +61 -0
- brkraw/dataclasses/study.py +131 -0
- brkraw/default/__init__.py +3 -0
- brkraw/default/pruner_specs/deid4share.yaml +42 -0
- brkraw/default/rules/00_default.yaml +4 -0
- brkraw/default/specs/metadata_dicom.yaml +236 -0
- brkraw/default/specs/metadata_transforms.py +92 -0
- brkraw/resolver/__init__.py +7 -0
- brkraw/resolver/affine.py +539 -0
- brkraw/resolver/datatype.py +69 -0
- brkraw/resolver/fid.py +90 -0
- brkraw/resolver/helpers.py +36 -0
- brkraw/resolver/image.py +188 -0
- brkraw/resolver/nifti.py +370 -0
- brkraw/resolver/shape.py +235 -0
- brkraw/schema/__init__.py +3 -0
- brkraw/schema/context_map.yaml +62 -0
- brkraw/schema/meta.yaml +57 -0
- brkraw/schema/niftiheader.yaml +95 -0
- brkraw/schema/pruner.yaml +55 -0
- brkraw/schema/remapper.yaml +128 -0
- brkraw/schema/rules.yaml +154 -0
- brkraw/specs/__init__.py +10 -0
- brkraw/specs/hook/__init__.py +12 -0
- brkraw/specs/hook/logic.py +31 -0
- brkraw/specs/hook/validator.py +22 -0
- brkraw/specs/meta/__init__.py +5 -0
- brkraw/specs/meta/validator.py +156 -0
- brkraw/specs/pruner/__init__.py +15 -0
- brkraw/specs/pruner/logic.py +361 -0
- brkraw/specs/pruner/validator.py +119 -0
- brkraw/specs/remapper/__init__.py +27 -0
- brkraw/specs/remapper/logic.py +924 -0
- brkraw/specs/remapper/validator.py +314 -0
- brkraw/specs/rules/__init__.py +6 -0
- brkraw/specs/rules/logic.py +263 -0
- brkraw/specs/rules/validator.py +103 -0
- brkraw-0.5.0.dist-info/METADATA +81 -0
- brkraw-0.5.0.dist-info/RECORD +88 -0
- {brkraw-0.3.11.dist-info → brkraw-0.5.0.dist-info}/WHEEL +1 -2
- brkraw-0.5.0.dist-info/entry_points.txt +13 -0
- brkraw/lib/__init__.py +0 -4
- brkraw/lib/backup.py +0 -641
- brkraw/lib/bids.py +0 -0
- brkraw/lib/errors.py +0 -125
- brkraw/lib/loader.py +0 -1220
- brkraw/lib/orient.py +0 -194
- brkraw/lib/parser.py +0 -48
- brkraw/lib/pvobj.py +0 -301
- brkraw/lib/reference.py +0 -245
- brkraw/lib/utils.py +0 -471
- brkraw/scripts/__init__.py +0 -0
- brkraw/scripts/brk_backup.py +0 -106
- brkraw/scripts/brkraw.py +0 -744
- brkraw/ui/__init__.py +0 -0
- brkraw/ui/config.py +0 -17
- brkraw/ui/main_win.py +0 -214
- brkraw/ui/previewer.py +0 -225
- brkraw/ui/scan_info.py +0 -72
- brkraw/ui/scan_list.py +0 -73
- brkraw/ui/subj_info.py +0 -128
- brkraw-0.3.11.dist-info/METADATA +0 -25
- brkraw-0.3.11.dist-info/RECORD +0 -28
- brkraw-0.3.11.dist-info/entry_points.txt +0 -3
- brkraw-0.3.11.dist-info/top_level.txt +0 -2
- tests/__init__.py +0 -0
- {brkraw-0.3.11.dist-info → brkraw-0.5.0.dist-info/licenses}/LICENSE +0 -0
brkraw/ui/subj_info.py
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import tkinter as tk
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from .config import font, button_size
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class LabelItem(tk.Frame):
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def set_label(self, text):
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self.label = tk.Label(self, text=text, width=8, anchor=tk.CENTER)
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self.entry = tk.Entry(self)
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anchor=tk.W, ipadx=5)
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self.entry.pack(side=tk.LEFT, fill=tk.X,
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anchor=tk.W, ipadx=5)
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self.label.configure(font=font)
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self.entry.config(width=16, font=font)
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def set_entry(self, text):
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self.entry.delete(0, tk.END)
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self.entry.insert(tk.END, '')
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self.entry.config(state=tk.DISABLED)
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else:
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self.entry.insert(tk.END, text)
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self.entry.config(state="readonly")
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class SubjInfo(tk.Frame):
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def __init__(self, *args, **kwargs):
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super(SubjInfo, self).__init__(*args, **kwargs)
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self._init_layout()
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self.config(padx=10)
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def _init_layout(self):
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self._upper_frame = tk.Frame(self)
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self._upper_frame.pack(side=tk.TOP, fill=tk.BOTH, expand=True, anchor=tk.CENTER)
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self._init_upper_frame()
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def _extend_layout(self):
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self._path_label = tk.Label(self._upper_frame, text='DataPath',
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width=button_size, font=font)
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self._path_label.pack(side=tk.LEFT, anchor=tk.E)
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# self._close = tk.Button(self._upper_frame, text='Close',
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# font=font, width=button_size)
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# self._close.pack(side=tk.RIGHT)
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self._refresh = tk.Button(self._upper_frame, text='Refresh',
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font=font, width=button_size)
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self._refresh.pack(side=tk.RIGHT)
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self._path = tk.Text(self._upper_frame, height=1, font=font)
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self._path.pack(side=tk.LEFT, fill=tk.BOTH, expand=True, anchor=tk.CENTER)
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self._path.config(state=tk.DISABLED)
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self._main_frame = tk.Frame(self)
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self._main_frame.pack(side=tk.TOP, fill=tk.BOTH, expand=True, anchor=tk.CENTER)
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self._init_main_frame()
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def _set_path(self, brkraw_obj):
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self._path.config(state=tk.NORMAL)
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self._path.insert(tk.END, brkraw_obj._pvobj.path)
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self._path.config(state=tk.DISABLED)
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def _clean_path(self):
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self._path.config(state=tk.NORMAL)
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self._path.config(state=tk.DISABLED)
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def _init_upper_frame(self):
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self._loadfile = tk.Button(self._upper_frame, text='Open File',
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font=font, width=button_size)
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self._loaddir = tk.Button(self._upper_frame, text='Open Directory',
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font=font, width=button_size)
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self._loadfile.pack(side=tk.LEFT)
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self._loaddir.pack(side=tk.LEFT)
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def _init_main_frame(self):
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self._c0 = tk.Frame(self._main_frame)
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self._c0.pack(side=tk.LEFT, fill=tk.X, anchor=tk.NW)
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self._c1 = tk.Frame(self._main_frame)
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self._c1.pack(side=tk.LEFT, fill=tk.X, anchor=tk.NW)
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self._c2 = tk.Frame(self._main_frame)
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self._c2.pack(side=tk.LEFT, fill=tk.X, anchor=tk.NW)
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self._c3 = tk.Frame(self._main_frame)
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self._c3.pack(side=tk.LEFT, fill=tk.X, anchor=tk.NW)
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self._init_labelitems()
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@staticmethod
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def _set_labelitem(frame, label, text=None):
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item = LabelItem(frame)
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item.pack(side=tk.TOP)
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item.set_label(label)
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item.set_entry(text)
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return item
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def _init_labelitems(self):
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self._account = self._set_labelitem(self._c0, 'Account')
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self._scandate = self._set_labelitem(self._c0, 'Scan Date')
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self._researcher = self._set_labelitem(self._c0, 'Researcher')
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self._subjectid = self._set_labelitem(self._c1, 'Subject ID')
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self._sessionid = self._set_labelitem(self._c1, 'Session ID')
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self._studyid = self._set_labelitem(self._c1, 'Study ID')
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self._dob = self._set_labelitem(self._c2, 'DOB')
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self._sex = self._set_labelitem(self._c2, 'Sex')
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self._weight = self._set_labelitem(self._c2, 'Weight')
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self._type = self._set_labelitem(self._c3, 'Type')
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self._position = self._set_labelitem(self._c3, 'Position')
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self._entry = self._set_labelitem(self._c3, 'Entry')
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def load_data(self, brkraw_obj):
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try:
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datetime = brkraw_obj.get_scan_time()
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except Exception:
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datetime = dict(date='N/A', start_time='N/A')
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pvobj = brkraw_obj._pvobj
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self._account.set_entry(pvobj.user_account)
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self._researcher.set_entry(pvobj.user_name)
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self._scandate.set_entry('{}, {}'.format(datetime['date'], datetime['start_time']))
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self._subjectid.set_entry(pvobj.subj_id)
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self._sessionid.set_entry(pvobj.session_id)
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self._studyid.set_entry(pvobj.study_id)
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self._dob.set_entry(pvobj.subj_dob)
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self._sex.set_entry(pvobj.subj_sex)
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self._weight.set_entry('{} kg'.format(pvobj.subj_weight))
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self._type.set_entry(pvobj.subj_type)
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self._position.set_entry(pvobj.subj_pose)
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self._entry.set_entry(pvobj.subj_entry)
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self._set_path(brkraw_obj)
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brkraw-0.3.11.dist-info/METADATA
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Metadata-Version: 2.1
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Name: brkraw
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Version: 0.3.11
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Summary: Bruker PvDataset Loader
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Home-page: https://github.com/brkraw/brkraw
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Author: SungHo Lee
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Author-email: shlee@unc.edu
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License: GNLv3
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Keywords: bruker data_handler converter administrator_tool
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Classifier: Development Status :: 5 - Production/Stable
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Classifier: Intended Audience :: Science/Research
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Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
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Classifier: Natural Language :: English
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Requires-Python: >3.5
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License-File: LICENSE
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Requires-Dist: nibabel (>=3.0.2)
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Requires-Dist: numpy (>=1.18.0)
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Requires-Dist: pandas (>=1.0.0)
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Requires-Dist: pillow (>=7.1.1)
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Requires-Dist: tqdm (>=4.45.0)
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Requires-Dist: openpyxl (>=3.0.3)
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Provides-Extra: simpleitk
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brkraw-0.3.11.dist-info/RECORD
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brkraw/__init__.py,sha256=g9TnXv5SSlqFNJIvxZRxEjpYXnXFuVBYtHFHd63jT58,133
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brkraw/lib/__init__.py,sha256=onx3VNjuyQlBvbw9WiynZ5jtjrgPzxRUTf8h7KWEFTE,82
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brkraw/lib/backup.py,sha256=HhqpAlyEGT9LPksXsSYRPmhrWEaZbRvxhGQYB7v228Q,28330
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brkraw/lib/bids.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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brkraw/lib/errors.py,sha256=atnEvonIIfhz2mekgzGWmCqGydZAt6G34dJpjWoaZ5Q,3978
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brkraw/lib/loader.py,sha256=i9XHQ7mwm5bxPN_L4vEnFzguZomNPFKljySPduXd8cM,54866
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brkraw/lib/orient.py,sha256=rp7rM7T0kM5xWqpE3ml2ghlmZ0qqEQ9bsoZYRgY6tI4,7108
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brkraw/lib/parser.py,sha256=hw4bkA1O45IYcc5gBe94GW8IPtB13vil2WTSh2beML8,1622
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brkraw/lib/pvobj.py,sha256=0DkIY9JQUvliLHQ1mMjOjuX1OjFH0y3g3m-VRHGW5mI,12833
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brkraw/lib/reference.py,sha256=DLErBjhF4yjVXOSdLfgG-JYngA3L_ert8964XoSDyqI,12647
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brkraw/scripts/brk_backup.py,sha256=NeEGuQDAIPTyU9F71LaHim8HGauoThbUEHh57kUPWJI,4335
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brkraw/scripts/brkraw.py,sha256=NIF3i-_32fnFgTBzquaBk48Ky8CrgocXDDG4YXWJwtM,37992
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brkraw/ui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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brkraw/ui/config.py,sha256=ThNW5VBUtdgxNIZjpBjDkkUPUHc6bytluE_ogujdYkY,419
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brkraw/ui/main_win.py,sha256=tJMcZYEChhjiMomebdTJRC4i2rUxM0QULpQv0lpJ9z4,8011
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brkraw/ui/previewer.py,sha256=CJ9Ff4AI7PHcADP0p6z_JywjwJOSYfBZ377eaXOPO_M,7777
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brkraw/ui/scan_info.py,sha256=C4kU-Xn4wVzrtOHy5sLI3VZ35g-TiD6lZopFOPF3Oyc,3684
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brkraw/ui/scan_list.py,sha256=REn3lclOh2CGhw1R4zF2vNkLgslg7iPGyVwD3PTVZF4,3503
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brkraw/ui/subj_info.py,sha256=7XgvUWG-KYJsfD6x7z3rGEsgS10DsHi6ARuIDdFyfkw,5467
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22
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tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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23
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brkraw-0.3.11.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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24
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brkraw-0.3.11.dist-info/METADATA,sha256=0ZOlyDNZ0jAhaIgEw9KIIIjXDio7SKf5iijxXqU4Q08,817
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25
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brkraw-0.3.11.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
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26
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-
brkraw-0.3.11.dist-info/entry_points.txt,sha256=9KKw06JUNuzHKwcBuEBqEi1HrH7f_vZYhgnrwR1pH6w,98
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27
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-
brkraw-0.3.11.dist-info/top_level.txt,sha256=kNjaAKdI6UKvDGAj7fI4RfHs84xpku5DcOXRUZPColY,13
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28
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-
brkraw-0.3.11.dist-info/RECORD,,
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tests/__init__.py
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