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An exercise to complete diagnostics code
These are two exercises for y'all to practice your Github workflow. First - make sure you have followed the instructions in the `README.md` file of your repository, to download the data, and commit the data hash file to the repositories. See <https://textbook.nipraxis.org/validating_data> for more detail. Next look at: * `scripts/validate_data.py` Fill out that file and make it run. Finally, look in the file: * `findoutlie/detectors.py` We recomend these pages as background. * https://textbook.nipraxis.org/on_modules.html * https://textbook.nipraxis.org/sys_path.html * https://textbook.nipraxis.org/assert.html * https://textbook.nipraxis.org/pathlib.html * https://textbook.nipraxis.org/docstrings.html * https://textbook.nipraxis.org/numpy_logical.html
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‎data/group-00/hash_list.txt‎

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‎findoutlie/detectors.py‎

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""" Utilities for detecting outliers
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These functions take a vector of values, and return a boolean vector of the
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same length as the input, where True indicates the corresponding value is an
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outlier.
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The outlier detection routines will likely be adapted to the specific measure
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that is being worked on. So, some detector functions will work on values > 0,
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other on normally distributed values etc. The routines should check that their
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requirements are met and raise an error otherwise.
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"""
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# Any imports you need
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# +++your code here+++
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def iqr_detector(measures, iqr_proportion=1.5):
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""" Detect outliers in `measures` using interquartile range.
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Returns a boolean vector of same length as `measures`, where True means the
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corresponding value in `measures` is an outlier.
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Call Q1, Q2 and Q3 the 25th, 50th and 75th percentiles of `measures`.
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The interquartile range (IQR) is Q3 - Q1.
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An outlier is any value in `measures` that is either:
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* > Q3 + IQR * `iqr_proportion` or
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* < Q1 - IQR * `iqr_proportion`.
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See: https://en.wikipedia.org/wiki/Interquartile_range
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Parameters
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----------
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measures : 1D array
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Values for which we will detect outliers
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iqr_proportion : float, optional
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Scalar to multiply the IQR to form upper and lower threshold (see
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above). Default is 1.5.
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Returns
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-------
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outlier_tf : 1D boolean array
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A boolean vector of same length as `measures`, where True means the
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corresponding value in `measures` is an outlier.
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"""
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# Any imports you need
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# Hints:
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# * investigate np.percentile
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# * You'll likely need np.logical_or
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# https://textbook.nipraxis.org/numpy_logical.html
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# +++your code here+++

‎findoutlie/spm_funcs.py‎

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"""
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This module defines functions implementing algorithms in SPM
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In the same directory as this file, you will find a 'tests' directory.
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Test this module with:
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python3 findoutlie/tests/test_spm_funcs.py
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or better, in IPython::
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%run findoutlie/tests/test_spm_funcs.py
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"""
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import numpy as np
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import nibabel as nib
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def spm_global(vol):
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""" Calculate SPM global metric for array `vol`
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Parameters
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----------
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vol : array
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Array giving image data, usually 3D.
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Returns
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-------
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g : float
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SPM global metric for `vol`
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"""
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T = np.mean(vol) / 8
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return np.mean(vol[vol > T])
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def get_spm_globals(fname):
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""" Calculate SPM global metrics for volumes in image filename `fname`
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Parameters
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----------
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fname : str
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Filename of file containing 4D image
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Returns
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-------
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spm_vals : array
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SPM global metric for each 3D volume in the 4D image.
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"""
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img = nib.load(fname)
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data = img.get_fdata()
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spm_vals = []
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for i in range(data.shape[-1]):
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vol = data[..., i]
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spm_vals.append(spm_global(vol))
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return np.array(spm_vals)

‎findoutlie/tests/ds107_sub012_t1r2_small.nii‎

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‎findoutlie/tests/get_global_signals.m‎

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% Get SPM global signal estimate for all volumes in smaller bold 4D
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file_volno = spm_select('ExtFPList', pwd, 'ds107_sub012_t1r2_small.nii', inf);
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V = spm_vol(file_volno);
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global_signals = ones([length(V), 1]);
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for i = 1:length(V)
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global_signals(i) = spm_global(V(i));
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end
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% Save signal values to a text file
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fid = fopen('global_signals.txt','w');
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fprintf(fid,'%6.2f\n', global_signals);
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fclose(fid);

‎findoutlie/tests/global_signals.txt‎

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376.53
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375.75
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375.26
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376.01
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376.83
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374.15
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372.54
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373.49
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374.23
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374.46

‎findoutlie/tests/test_detectors.py‎

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""" Test script for detector functions
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Run these tests with::
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python3 findoutlie/tests/test_detectors.py
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or better, in IPython::
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%run findoutlie/tests/test_detectors.py
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"""
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from pathlib import Path
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import sys
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MY_DIR = Path(__file__).parent
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# Here you should add the directory containing the findoutlie
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# directory to the Python path.
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# Hint: sys.path
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# Hint: see the solutions if you are stuck.
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# +++your code here+++
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import numpy as np
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# This import needs the directory containing the findoutlie directory
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# on the Python path.
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from detectors import iqr_detector
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def test_iqr_detector():
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# From: http://www.purplemath.com/modules/boxwhisk3.htm
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example_values = np.array(
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[10.2, 14.1, 14.4, 14.4, 14.4, 14.5, 14.5, 14.6, 14.7, 14.7, 14.7,
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14.9, 15.1, 15.9, 16.4])
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is_outlier = iqr_detector(example_values, 1.5)
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assert np.all(example_values[is_outlier] == [10.2, 15.9, 16.4])
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# Test not-default value for outlier proportion
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is_outlier = iqr_detector(example_values, 0.5)
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assert np.all(example_values[is_outlier] == [10.2, 14.1, 15.1, 15.9, 16.4])
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if __name__ == '__main__':
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# File being executed as a script
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test_iqr_detector()
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print('Tests passed')

‎findoutlie/tests/test_spm_funcs.py‎

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""" Test script for SPM functions
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Run these tests with::
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python3 findoutlie/tests/test_spm_funcs.py
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or better, in IPython::
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%run findoutlie/tests/test_spm_funcs.py
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"""
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from pathlib import Path
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import sys
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MY_DIR = Path(__file__).parent
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EXAMPLE_FILENAME = 'ds107_sub012_t1r2_small.nii'
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# Here you should add the directory containing the findoutlie
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# directory to the Python path.
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# Hint: sys.path
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# Hint: see the solutions if you are stuck.
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# +++your code here+++
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import numpy as np
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import nibabel as nib
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# This import needs the directory containing the findoutlie directory
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# on the Python path.
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from spm_funcs import get_spm_globals, spm_global
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def test_spm_globals():
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# Test get_spm_globals and spm_global functions
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example_path = MY_DIR / EXAMPLE_FILENAME
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expected_values = np.loadtxt(MY_DIR / 'global_signals.txt')
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glob_vals = get_spm_globals(example_path)
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assert glob_vals is not None, 'Did you forget to return the values?'
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assert np.allclose(glob_vals, expected_values, rtol=1e-4)
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img = nib.load(example_path)
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data = img.get_fdata()
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globals = []
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for vol_no in range(data.shape[-1]):
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vol = data[..., vol_no]
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globals.append(spm_global(vol))
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assert np.allclose(globals, expected_values, rtol=1e-4)
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if __name__ == '__main__':
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# File being executed as a script
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test_spm_globals()
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print('Tests passed')

‎scripts/validate_data.py‎

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Run as:
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python3 scripts/validata_data.py data
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python3 scripts/validate_data.py
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"""
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from pathlib import Path
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import sys
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import hashlib
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def file_hash(filename):
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""" Get byte contents of file `filename`, return SHA1 hash
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@@ -53,19 +53,22 @@ def validate_data(data_directory):
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# If hash for filename is not the same as the one in the file, raise
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# ValueError
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# This is a placeholder, replace it to write your solution.
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raise NotImplementedError('This is just a template -- you are expected to code this.')
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raise NotImplementedError(
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'This is just a template -- fill out the template with code.')
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def main():
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# This function (main) called when this file run as a script.
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#
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# Get the data directory from the command line arguments
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if len(sys.argv) < 2:
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raise RuntimeError("Please give data directory on "
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"command line")
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data_directory = sys.argv[1]
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group_directory = (Path(__file__).parent.parent / 'data')
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groups = list(group_directory.glob('group-??'))
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if len(groups) == 0:
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raise RuntimeError('No group directory in data directory: '
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'have you downloaded and unpacked the data?')
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if len(groups) > 1:
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raise RuntimeError('Too many group directories in data directory')
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# Call function to validate data in data directory
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validate_data(data_directory)
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validate_data(groups[0])
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if __name__ == '__main__':

‎solutions/.solutions.toml‎

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[solution.validate_data]
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out_path = '{one_down}/scripts/validate_data.py'
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[solution.test_spm_funcs]
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out_path = '{one_down}/findoutlie/tests/test_spm_funcs.py'
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[solution.detectors]
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out_path = '{one_down}/findoutlie/detectors.py'
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[solution.test_detectors]
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out_path = '{one_down}/findoutlie/tests/test_detectors.py'

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