Multiprocess fitting script

WrapImage/nifti_wrapper.py

@@ -1,64 +1,13 @@
 import argparse
-import json
-import os
-import nibabel as nib
+from utilities.process.file_io import read_nifti_file, read_bval_file, read_bvec_file, save_nifti_file
+from utilities.process.diffusion_utils import find_directions, find_shells, normalize_series
 from src.wrappers.OsipiBase import OsipiBase
 import numpy as np
 from tqdm import tqdm
+from tqdm.contrib.concurrent import process_map
+from functools import partial
 
 
-def read_nifti_file(input_file):
-    """
-    For reading the 4d nifti image
-    """
-    nifti_img = nib.load(input_file)
-    return nifti_img.get_fdata(), nifti_img.header
-
-def read_json_file(json_file):
-    """
-    For reading the json file
-    """
-
-    if not os.path.exists(json_file):
-        raise FileNotFoundError(f"File '{json_file}' not found.")
-
-    with open(json_file, "r") as f:
-        try:
-            json_data = json.load(f)
-        except json.JSONDecodeError as e:
-            raise ValueError(f"Error decoding JSON in file '{json_file}': {e}")
-
-    return json_data
-
-def read_bval_file(bval_file):
-    """
-    For reading the bval file
-    """
-    if not os.path.exists(bval_file):
-        raise FileNotFoundError(f"File '{bval_file}' not found.")
-
-    bval_data = np.genfromtxt(bval_file, dtype=float)
-    return bval_data
-
-def read_bvec_file(bvec_file):
-    """
-    For reading the bvec file
-    """
-    if not os.path.exists(bvec_file):
-        raise FileNotFoundError(f"File '{bvec_file}' not found.")
-
-    bvec_data = np.genfromtxt(bvec_file)
-    bvec_data = np.transpose(bvec_data)  # Transpose the array
-    return bvec_data
-
-def save_nifti_file(data, output_file, affine=None, **kwargs):
-    """
-    For saving the 3d nifti images of the output of the algorithm
-    """
-    if affine is None:
-        affine = np.eye(data.ndim + 1)
-    output_img = nib.nifti1.Nifti1Image(data, affine , **kwargs)
-    nib.save(output_img, output_file)
 
 def loop_over_first_n_minus_1_dimensions(arr):
     """
@@ -75,52 +24,162 @@ def loop_over_first_n_minus_1_dimensions(arr):
         flat_view = arr[idx].flatten()
         yield idx, flat_view
 
+def generate_data(data, bvals, b0_indices, groups, total_iteration):
+    num_directions = groups.shape[1]
+    data = data.reshape(total_iteration, -1)
+    for idx in range(total_iteration):
+        for dir in range(num_directions):
+            # print('yielding')
+            yield (data[idx, groups[:, dir]].flatten(), bvals[:, groups[:, dir]].ravel(), b0_indices[:, groups[:, dir]].ravel())
+
+def osipi_fit(fitfunc, data_bvals):
+    data, bvals, b0_indices = data_bvals
+    data = normalize_series(data, b0_indices)
+    # print(f'data.shape {data.shape} data {data} bvals {bvals}')
+    return fitfunc(data, bvals)
+
+# def osipi_fit(fitfunc, bvals, data, f_image, Dp_image, D_image, index):
+#     bval_index = len(f_image) % len(bvals)
+#     print(f'data.shape {data.shape} index {index} data[index] {data[index]} bvals.shape {bvals.shape} bval_index {bval_index} bvals {bvals[:, bval_index]}')
+#     [f_fit, Dp_fit, D_fit] = fitfunc(data[index], bvals[:, bval_index])
+#     f_image[index] = f_fit
+#     Dp_image[index] = Dp_fit
+#     D_image[index] = D_fit
+
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Read a 4D NIfTI phantom file along with BIDS JSON, b-vector, and b-value files.")
     parser.add_argument("input_file", type=str, help="Path to the input 4D NIfTI file.")
     parser.add_argument("bvec_file", type=str, help="Path to the b-vector file.")
     parser.add_argument("bval_file", type=str, help="Path to the b-value file.")
-    parser.add_argument("--affine", type=float, nargs="+", help="Affine matrix for NIfTI image.")
+    parser.add_argument("--nproc", type=int, default=0, help="Number of processes to use, -1 disabled multprocessing, 0 automatically determines number, >0 uses that number.")
+    parser.add_argument("--group_directions", default=False, action="store_true", help="Fit all directions together")
+    parser.add_argument("--affine", type=float, default=None, nargs="+", help="Affine matrix for NIfTI image.")
     parser.add_argument("--algorithm", type=str, default="OJ_GU_seg", help="Select the algorithm to use.")
-    parser.add_argument("--algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.")
+    parser.add_argument("--algorithm_args", default={}, nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.")
+
 
     args = parser.parse_args()
 
     try:
         # Read the 4D NIfTI file
         data, _ = read_nifti_file(args.input_file)
+        data = data[0::4, 0::4, 0::2, :]
+        print(f'data.shape {data.shape}')
 
         # Read the b-vector, and b-value files
         bvecs = read_bvec_file(args.bvec_file)
         bvals = read_bval_file(args.bval_file)
+        # print(f'bvals.size {bvals.shape} bvecs.size {bvecs.shape}')
+        print(bvals)
+        print(bvecs)
+        shells, bval_indices, b0_indices = find_shells(bvals)
+        num_b0 = np.count_nonzero(b0_indices)
+        print(shells)
+        print(bval_indices)
+        # print(b0_indices)
+        # print(bvecs)
+
+        # print('vectors')
+        vectors, bvec_indices, groups = find_directions(bvecs, b0_indices)
+        print(vectors)
+        print(bvec_indices)
+        print(f'groups {groups}')
+
+        # split_bval_bvec(bvec_indices, num_vectors)
+        # quit()
+
 
         # Pass additional arguments to the algorithm
-
-        fit = OsipiBase(algorithm=args.algorithm)
-        f_image = []
-        Dp_image = []
-        D_image = []
+        fit = OsipiBase(algorithm=args.algorithm, **args.algorithm_args)
+
+        # n = data.ndim
+        output_shape = list(data.shape[:-1])
+        # if args.group_directions:
+        #     input_data = data
+        #     input_bvals = np.atleast_2d(bvals)
+        # else:
+        #     num_directions = groups.shape[1]
+        #     measurements = np.count_nonzero(groups[:, 0])
+        #     print(f"group_length {num_directions}")
+        #     input_shape = output_shape.copy()
+
+        #     print(f"groups[:, 0] {groups[:,0]} {np.count_nonzero(groups[:, 0])}")
+        #     input_shape.append(num_directions)
+        #     input_shape.append(measurements)
+        #     output_shape.append(num_directions)
+        #     print(f"input_shape {input_shape}")
+        #     input_data = np.zeros(input_shape)
+        #     input_bvals = np.zeros([measurements, num_directions])
+        #     for group_idx in range(num_directions):
+        #         print(f"group {group_idx} {groups[:, group_idx]}")
+        #         input_data[..., group_idx, :] = data[..., groups[:, group_idx]]
+        #         input_bvals[:, group_idx] = bvals[groups[:, group_idx]]
+        # if args.group_directions:
+        #     input_data = data
+        #     input_bvals = np.atleast_2d(bvals)
+        # else:
+        input_data = data
+        input_bvals = np.atleast_2d(bvals)
+        b0_indices = np.atleast_2d(b0_indices)
+        print(f"data.shape {data.shape}")
+        print(f"input_data.shape {input_data.shape}")
+
+
+
+
+        voxel_iteration = np.prod(output_shape)
+        group_iteration = groups.shape[1]
+        total_iteration = voxel_iteration * group_iteration
+        output_shape.append(group_iteration)
+        f_image = np.zeros(output_shape)
+        Dp_image = np.zeros(output_shape)
+        D_image = np.zeros(output_shape)
+        print(f_image.shape)
 
         # This is necessary for the tqdm to display progress bar.
-        n = data.ndim
-        total_iteration = np.prod(data.shape[:n-1])
-        for idx, view in tqdm(loop_over_first_n_minus_1_dimensions(data), desc=f"{args.algorithm} is fitting", dynamic_ncols=True, total=total_iteration):
-            [f_fit, Dp_fit, D_fit] = fit.osipi_fit(view, bvals)
-            f_image.append(f_fit)
-            Dp_image.append(Dp_fit)
-            D_image.append(D_fit)
-
-        # Convert lists to NumPy arrays
-        f_image = np.array(f_image)
-        Dp_image = np.array(Dp_image)
-        D_image = np.array(D_image)
-
-        # Reshape arrays if needed
-        f_image = f_image.reshape(data.shape[:data.ndim-1])
-        Dp_image = Dp_image.reshape(data.shape[:data.ndim-1])
-        D_image = D_image.reshape(data.shape[:data.ndim-1])
+
+        # total_iteration = np.prod(data.shape[:n-1])
+        print(f'input_bvals {input_bvals}')
+        print(f'voxel_iteration {voxel_iteration} input_data.shape {input_data.shape}')
+        # print(f'input_data[5000] {input_data.reshape(total_iteration, -1)[5000]}')
+
+
+        # fit_partial = partial(osipi_fit, fit.osipi_fit, input_bvals, input_data.reshape(total_iteration, -1), f_image.reshape(total_iteration), Dp_image.reshape(total_iteration), D_image.reshape(total_iteration))
+        fit_partial = partial(osipi_fit, fit.osipi_fit)
+
+
+        if args.nproc >= 0:
+            print('multiprocess fitting')
+            gd = generate_data(input_data, input_bvals, b0_indices, groups, voxel_iteration)
+            map_args = [fit_partial, gd]
+            chunksize = round(total_iteration / args.nproc) if args.nproc > 0 else round(total_iteration / 128)
+            print(f'chunksize {chunksize}')
+            map_kwargs = {'desc':f"{args.algorithm} is fitting", 'dynamic_ncols':True, 'total':total_iteration, 'chunksize':chunksize}
+            if args.nproc > 0:
+                map_kwargs['max_workers'] = args.nproc
+            result = process_map(*map_args, **map_kwargs)
+            output = np.asarray(result)
+            print(f'output.shape {output.shape}')
+            output = output.reshape([*output_shape, 3])
+            f_image = output[..., 0]
+            print(f'f_img.shape {f_image.shape}')
+            Dp_image = output[..., 1]
+            D_image = output[..., 2]
+            # print(result)
+            # if args.nproc == 0:  # TODO: can this be done more elegantly, I just want to omit a single parameter here
+            #     process_map(fit_partial, range(total_iteration), desc=f"{args.algorithm} is fitting", dynamic_ncols=True, total=total_iteration)
+            # else:
+            #     process_map(fit_partial, range(total_iteration), max_workers=args.nproc, desc=f"{args.algorithm} is fitting", dynamic_ncols=True, total=total_iteration)
+        else:
+            for idx, view in tqdm(loop_over_first_n_minus_1_dimensions(data), desc=f"{args.algorithm} is fitting", dynamic_ncols=True, total=total_iteration):
+                [f_fit, Dp_fit, D_fit] = fit.osipi_fit(view, bvals)
+                f_image[idx] = f_fit
+                Dp_image[idx] = Dp_fit
+                D_image[idx] = D_fit
+
+        print("finished fitting")
 
         save_nifti_file(f_image, "f.nii.gz", args.affine)
         save_nifti_file(Dp_image, "dp.nii.gz", args.affine)

conftest.py

@@ -2,6 +2,10 @@
 import pathlib
 import json
 import csv
+import tempfile
+import os
+import random
+import numpy as np
 # import datetime
 
 
@@ -178,3 +182,45 @@ def data_list(filename):
     bvals = bvals['bvalues']
     for name, data in all_data.items():
         yield name, bvals, data
+
+@pytest.fixture
+def bval_bvec_info():
+    shells = [0, 10, 20, 50, 100, 200, 500, 1000]
+    # random.shuffle(shells)
+    bvals = np.concatenate((shells, random.choices(shells, k=10)), axis=0)
+
+    vecs = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1], [0.707, 0.707, 0], [0.5, 0.5, 0.5], [0, 0.707, 0.707], [0.707, 0, 0.707]]
+    for idx in range(len(vecs)):
+        if np.linalg.norm(vecs[idx]) != 0:
+            vecs[idx] = vecs[idx]/np.linalg.norm(vecs[idx])
+    bvecs = []
+    vecs_idx = 1  # the first index is needed for the true output, but not needed here
+    for idx in range(len(bvals)):
+        if bvals[idx] == 0:
+            bvecs.append(np.asarray([0, 0, 0]))
+        elif vecs_idx < len(vecs):
+            bvecs.append(vecs[vecs_idx])
+            vecs_idx += 1
+        else:
+            bvecs.append(random.choice(vecs[1:]))  # don't put a b0 in where it shouldn't be
+    print(f'raw bvals {bvals}')
+    print(f'raw bvecs {bvecs}')
+
+
+    with tempfile.NamedTemporaryFile(mode='wt', delete=False) as fp_val, tempfile.NamedTemporaryFile(mode='wt', delete=False) as fp_vec:
+        writer = csv.writer(fp_val, delimiter=' ')
+        for bval in bvals:
+            writer.writerow((bval,))
+        fp_val.close()
+        writer = csv.writer(fp_vec, delimiter=' ')
+        for bvec in bvecs:
+            writer.writerow(bvec)
+        fp_vec.close()
+        yield (fp_val.name, np.asarray(shells), bvals, fp_vec.name, np.asarray(vecs), np.asarray(bvecs))
+        os.unlink(fp_val.name)  # use NamedTemporaryFile with delete_on_close with later python versions
+        os.path.exists(fp_val.name)
+        os.unlink(fp_vec.name)  # use NamedTemporaryFile with delete_on_close with later python versions
+        os.path.exists(fp_vec.name)
+
+
+

tests/utilities/unit_tests/test_diffusion_utils.py

@@ -0,0 +1,54 @@
+import numpy as np
+import numpy.testing as npt
+from utilities.process.file_io import read_bval_file, read_bvec_file
+from utilities.process.diffusion_utils import find_shells, find_directions, normalize_series
+
+
+#TODO: test without b0
+#TODO: test symmetry
+def test_read_bval_bvec(bval_bvec_info):
+    bval_name, shells, bvals, bvec_name, directions, bvecs = bval_bvec_info
+    saved_bvals = read_bval_file(bval_name)
+    npt.assert_equal(bvals, np.asarray(saved_bvals))
+    saved_shells, bval_indices, b0 = find_shells(saved_bvals)
+    npt.assert_equal(shells, saved_shells, "Shells do not match")
+    npt.assert_equal(saved_bvals, [saved_shells[index] for index in bval_indices], "Bvalue indices are incorrect")
+
+    saved_bvecs = read_bvec_file(bvec_name)
+    npt.assert_allclose(np.asarray(bvecs), np.asarray(saved_bvecs), err_msg="Incorrectly saved bvectors")
+    vectors, bvec_indices, groups = find_directions(saved_bvecs, b0)
+    assert vectors.shape[0] == groups.shape[1] + 1, "Number of vectors is correct"
+    assert vectors.shape == np.asarray(directions).shape, "Number of elements in directions does not match"
+    directions_set = set()
+    for direction in directions:
+        directions_set.add(tuple(direction))
+    vectors_set = set()
+    for vector in vectors:
+        vectors_set.add(tuple(vector))
+    assert directions_set == vectors_set, "Elements in directions does not match"
+    npt.assert_equal(saved_bvecs, [vectors[index] for index in bvec_indices], "Bvector indices are incorrect")
+
+def test_normalization():
+    original = np.atleast_2d([[10, 10], [10, 10], [5, 5], [5, 5]]).T
+
+    indices = [True, False, False, False]
+    updated = normalize_series(original.copy(), indices)
+    npt.assert_allclose(original / 10, updated, err_msg="Normalization with 1 point failed")
+
+    indices = [True, True, False, False]
+    updated = normalize_series(original.copy(), indices)
+    npt.assert_allclose(original / 10, updated, err_msg="Normalization with 2 points failed")
+
+    indices = [False, True, True, False]
+    updated = normalize_series(original.copy(), indices)
+    npt.assert_allclose(original / 7.5, updated, err_msg="Normalization with 2 different points failed")
+
+    indices = [False, False, False, True]
+    updated = normalize_series(original.copy(), indices)
+    npt.assert_allclose(original / 5, updated, err_msg="Normalization with 1 final point failed")
+
+    original = np.asarray([10, 5])
+    indices = [True, False]
+
+    updated = normalize_series(original.copy(), indices)
+    npt.assert_allclose(original / 10, updated, err_msg="Normalization of 1D failed")

tests/utilities/unit_tests/test_file_io.py

@@ -0,0 +1,23 @@
+import tempfile
+import os
+import numpy as np
+import numpy.testing as npt
+from utilities.process.file_io import save_nifti_file, read_nifti_file, read_bval_file, read_bvec_file
+
+
+def test_nifti_read_write():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = os.path.join(tmp, 'my_nifti.nii.gz')
+        data = np.random.rand(7, 8, 9)
+        save_nifti_file(data, path)
+        assert os.path.exists(path), "Nifti file does not exist"
+        saved_data, saved_hdr = read_nifti_file(path)
+        npt.assert_equal(data, saved_data, "Nifti data does not match")
+
+def test_read_bval_bvec(bval_bvec_info):
+    bval_name, shells, bvals, bvec_name, directions, bvecs = bval_bvec_info
+    assert bvecs.shape[1] == 3, "Bvec input is not Nx3"
+    saved_bvals = read_bval_file(bval_name)
+    npt.assert_equal(bvals, np.asarray(saved_bvals), "Bvalues do not match")
+    saved_bvecs = read_bvec_file(bvec_name)
+    npt.assert_allclose(bvecs, np.asarray(saved_bvecs), err_msg="Bvectors do not match")