Merge 675808b into 4c08d99

code/utils/functions/mask_functions.py

@@ -0,0 +1,126 @@
+"""mask_functions.py
+
+A collection of functions to make masks on data.
+See test_* functions in this directory for nose tests
+"""
+from __future__ import print_function, division
+
+import sys, os, pdb
+import numpy as np
+import nibabel as nib
+import numpy.linalg as npl
+
+from os.path import splitext
+from numpy.testing import assert_array_equal
+from scipy.ndimage import affine_transform
+
+
+def make_mask_filtered_data(func_path, mask_path):
+    """Return the masked filtered data
+
+    Parameters
+    ----------
+    func_path: string
+    	  path to the 4D data
+    
+    mask_path: string
+        path to the mask function
+
+    Return
+    ------
+    masked_func: 4D array
+        masked filtered data
+    
+    """
+    func_img = nib.load(func_path)
+    mask_img = nib.load(mask_path)
+    mask = mask_img.get_data()
+    func_data = func_img.get_data()
+    # Make data 4D to prepare for "broadcasting"
+    mask = np.reshape(mask, mask.shape + (1,))
+    # "Broadcasting" expands the final length 1 dimension to match the func data
+    masked_func = nib.Nifti1Image(func_data, func_img.affine, func_img.header)
+    # nib.save(masked_func, 'masked_' + img_name )
+    return masked_func
+
+def make_binary_mask(data, mask_bool):
+    """Return a numpy array with 0 and 1 
+    Parameters
+    ----------
+
+    Return
+    ------
+    """
+    data = np.asarray(data)
+    mask_bool = np.asarray(mask_bool)
+    assert(len(data.shape) == len(mask_bool.shape)),\
+    "Data and mask shape differ \n" \
+    + "Data dim is: %s\nMask dim is: %s" \
+    %(len(data.shape), len(mask_bool.shape))
+    assert(all(data.shape[i] >= mask_bool.shape[i] \
+           for i in range(len(data.shape)))),\
+    "Data and mask shape are not compatible"\
+    +"Data shape is: %s\nMask shape is: %s"\
+    %(data.shape, mask_bool.shape)
+    new_mask = np.zeros(data.shape)
+    new_mask[mask_bool] = 1
+    return new_mask 
+
+
+def resample_filtered_data(func_path, template_path):
+    """Resample template to filtered functional dataset
+    
+    Parameters
+    ----------
+    func_path: string
+        path of the 4D filtered data to resample
+    template_path: string
+        path to the template to apply on the data
+    
+    """
+    filtered_func = nib.load(func_path) 
+    filtered_shape = filtered_func.shape[:3]
+    template_img = nib.load(mni_fname)
+    template_data = template_img.get_data()
+    vox2vox = npl.inv(template_img.affine).dot(filtered_func.affine)
+    M, trans = nib.affines.to_matvec(vox2vox)
+    resampled = affine_transform(template_data, M, trans,
+                                 output_shape=filtered_shape)
+    froot, ext = splitext(mni_fname)
+    new_name = froot + '_2mm' + ext
+    new_img = nib.Nifti1Image(resampled, filtered_func.affine,
+                              template_img.header)
+    #nib.save(new_img, new_name) 
+    return new_img
+
+def apply_mask(data, mask):
+    """Apply mask on an image and return the masked data
+
+    Parameters
+    ----------
+    data: numpy array
+        The subject's run image data
+    mask: numpy array same shape as data  
+        The mask for the corresponding data_3d
+        has 1 for the positions to select and 
+      	0 for the positions to filter out.
+    Return
+    ------
+    masked_data: numpy array 
+        Array with the values of the data at the selected positions
+	and 0 for the position filtered out by the mask.
+    """
+    assert(data.shape == mask.shape), "Data and mask shape differ \n" \
+    + "Data shape i: %s\nMask shape is: %s" %(data.shape, mask.shape)
+    return data * mask 
+
+if __name__=='__main__':
+    slab0 = np.reshape(np.arange(9), (3, 3))
+    slab1 = np.reshape(np.arange(100, 109), (3, 3))
+    arr_3d = np.zeros((2, 3, 3))
+    arr_3d[0, :, :] = slab0
+    arr_3d[1, :, :] = slab1
+    arr_2d = np.arange(9).reshape((3,3))
+    mask_bool2d = arr_2d < 10
+    make_binary_mask(arr_3d,mask_bool2d)
+    pdb.set_trace()

code/utils/tests/test_mask.py

@@ -0,0 +1,51 @@
+"""test_mask.py
+Tests for the functions in the mask_functions.py
+
+Run with:
+    nosetests test_mask.py
+"""
+from __future__ import print_function
+import os, sys
+import numpy as np
+from numpy.testing import assert_array_equal
+
+#Append path to functions
+sys.path.append(os.path.join(os.path.dirname(__file__), "../functions/"))
+from mask_functions import *
+
+
+def test_apply_mask():
+    # We make a 3D array of shape (3,3,2)
+    slab0 = np.reshape(np.arange(9), (3, 3))
+    slab1 = np.reshape(np.arange(100, 109), (3, 3))
+    arr_3d = np.zeros((2, 3, 3))
+    arr_3d[0, :, :] = slab0
+    arr_3d[1, :, :] = slab1
+    # We make a mask as a 3D array of shape (2,3,3)
+    # with zeros on the 2nd component of the 1st dimension
+    mask_3d = np.zeros((2, 3, 3))
+    mask_3d[0] = np.ones((3,3))
+    # Defined the resulting masked array
+    masked_arr = np.zeros((2,3,3))
+    masked_arr[0, :, :] = slab0
+    assert_array_equal(apply_mask(arr_3d, mask_3d),masked_arr)
+
+
+def test_make_binary_mask():
+    # We make a 3D array of shape (3,3,2)
+    slab0 = np.reshape(np.arange(9), (3, 3))
+    slab1 = np.reshape(np.arange(100, 109), (3, 3))
+    arr_3d = np.zeros((2, 3, 3))
+    arr_3d[0, :, :] = slab0
+    arr_3d[1, :, :] = slab1
+    # We make a mask boolean as a 3D array of shape (2,3,3)
+    # that filtered the values below 100
+    mask_bool = arr_3d < 100
+    mask_3d = np.zeros((2, 3, 3))
+    mask_3d[0] = np.ones((3,3))
+    assert_array_equal(make_binary_mask(arr_3d,mask_bool), mask_3d)
+    arr_2d = np.arange(9).reshape((3,3))
+    mask_bool2d = arr_2d < 10
+#    make_binary_mask(arr_3d,mask_bool2d)
+
+