Fix detectors & dvars

README.md

@@ -8,7 +8,7 @@ You should put the code in this `findoutlie` directory on your Python PATH.
 
 This README file has instructions on how to get, validate and process the data.
 
-# Added this new line.
+# Instructions
 
 ## Get the data
 

data/group-02/hash_list.txt

@@ -0,0 +1,40 @@
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findoutlie/detectors.py

@@ -11,7 +11,7 @@
 """
 
 # Any imports you need
-# +++your code here+++
+import numpy as np
 
 
 def iqr_detector(measures, iqr_proportion=1.5):
@@ -45,9 +45,9 @@ def iqr_detector(measures, iqr_proportion=1.5):
         A boolean vector of same length as `measures`, where True means the
         corresponding value in `measures` is an outlier.
     """
-    # Any imports you need
-    # Hints:
-    # * investigate np.percentile
-    # * You'll likely need np.logical_or
-    # https://textbook.nipraxis.org/numpy_logical.html
-    # +++your code here+++
+    Q1, Q3 = np.percentile(measures, [25, 75])
+    IQR = Q3 - Q1
+    lower_lim = Q1 - IQR * iqr_proportion
+    upper_lim = Q3 + IQR * iqr_proportion
+    is_outlier = np.logical_or(measures<lower_lim, measures>upper_lim)
+    return is_outlier

findoutlie/metrics.py

@@ -1,8 +1,7 @@
 """ Scan outlier metrics
 """
 
-# Any imports you need
-# +++your code here+++
+import numpy as np
 
 
 def dvars(img):
@@ -26,7 +25,8 @@ def dvars(img):
     # In [3]: np.mean(arr, axis=1)
     # Out[2]: array([3., 6.])
     #
-    # You may be be able to solve this in four lines, without a loop.
-    # But solve it any way you can.
-    # This is a placeholder, replace it to write your solution.
-    raise NotImplementedError('Code up this function')
+    data = img.get_fdata()
+    vol_diff = np.diff(data, axis=3) # [x,y,z,t-1]
+    dvar_val = np.sqrt(np.mean(vol_diff ** 2, axis=(0,1,2)))
+
+    return dvar_val

scripts/validate_data.py

@@ -23,10 +23,11 @@ def file_hash(filename):
         SHA1 hexadecimal hash string for contents of `filename`.
     """
     # Open the file, read contents as bytes.
+    pth = Path(filename)
+    file_bytes = pth.read_bytes()
     # Calculate, return SHA1 has on the bytes from the file.
-    # This is a placeholder, replace it to write your solution.
-    raise NotImplementedError(
-        'This is just a template -- you are expected to code this.')
+    return hashlib.sha1(file_bytes).hexdigest()
+
 
 
 def validate_data(data_directory):
@@ -48,13 +49,17 @@ def validate_data(data_directory):
         ``data_hashes.txt`` file.
     """
     # Read lines from ``data_hashes.txt`` file.
-    # Split into SHA1 hash and filename
-    # Calculate actual hash for given filename.
-    # If hash for filename is not the same as the one in the file, raise
-    # ValueError
-    # This is a placeholder, replace it to write your solution.
-    raise NotImplementedError(
-        'This is just a template -- fill out the template with code.')
+    hash_path = Path(data_directory) / 'hash_list.txt'
+    with open(hash_path, 'r') as f:
+        for line in f.readlines():
+            # Split into SHA1 hash and filename
+            read_hash, filename = line.strip().split()
+            # Calculate actual hash for given filename.
+            true_hash = file_hash(hash_path.parent.parent / filename)
+            # If hash for filename is not the same as the one in the file, raise
+            if true_hash != read_hash:
+                raise ValueError("Hash value not as recorded.")
+
 
 
 def main():