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utils.py
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utils.py
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"""Utility functions for NiMARE."""
import contextlib
import datetime
import inspect
import json
import logging
import multiprocessing as mp
import os
import os.path as op
import re
import warnings
from functools import wraps
from string import ascii_lowercase
from tempfile import mkstemp
import joblib
import nibabel as nib
import numpy as np
import pandas as pd
from nilearn._utils import check_niimg_3d
from nilearn._utils.niimg import _safe_get_data
from nilearn.image import new_img_like, resampling, threshold_img
from nilearn.input_data import NiftiMasker
from scipy.ndimage import (
center_of_mass,
generate_binary_structure,
label,
maximum_filter,
minimum_filter,
)
LGR = logging.getLogger(__name__)
def _check_ncores(n_cores):
"""Check number of cores used for method.
.. versionadded:: 0.0.12
Moved from Estimator._check_ncores into its own function.
"""
if n_cores <= 0:
n_cores = mp.cpu_count()
elif n_cores > mp.cpu_count():
LGR.warning(
f"Desired number of cores ({n_cores}) greater than number "
f"available ({mp.cpu_count()}). Setting to {mp.cpu_count()}."
)
n_cores = mp.cpu_count()
return n_cores
def get_resource_path():
"""Return the path to general resources, terminated with separator.
Resources are kept outside package folder in "datasets".
Based on function by Yaroslav Halchenko used in Neurosynth Python package.
"""
return op.abspath(op.join(op.dirname(__file__), "resources") + op.sep)
def get_template(space="mni152_2mm", mask=None):
"""Load template file.
.. versionchanged:: 0.0.11
- Remove the ``mask="gm"`` option.
- Replace the nilearn templates with ones downloaded directly from TemplateFlow.
Parameters
----------
space : {'mni152_1mm', 'mni152_2mm', 'ale_2mm'}, optional
Template to load. Default is 'mni152_2mm'.
The options are:
- mni152_1mm: The MNI152NLin6Asym template at 1mm3 resolution,
downloaded from TemplateFlow. The shape of this template is 182x218x182 voxels.
- mni152_2mm: The MNI152NLin6Asym template at 2mm3 resolution,
downloaded from TemplateFlow. The shape of this template is 91x109x91 voxels.
- ale_2mm: The template used is the MNI152NLin6Asym template at 2mm3 resolution,
but if ``mask='brain'``, then a brain mask taken from GingerALE will be used.
The brain mask corresponds to GingerALE's "more conservative" mask.
The shape of this template is 91x109x91 voxels.
mask : {None, 'brain'}, optional
Whether to return the raw T1w template (None) or a brain mask ('brain').
Default is None.
Returns
-------
img : :obj:`~nibabel.nifti1.Nifti1Image`
Template image object.
"""
template_dir = op.join(get_resource_path(), "templates")
if space == "mni152_1mm":
if mask is None:
img = nib.load(op.join(template_dir, "tpl-MNI152NLin6Asym_res-01_T1w.nii.gz"))
elif mask == "brain":
img = nib.load(
op.join(template_dir, "tpl-MNI152NLin6Asym_res-01_desc-brain_mask.nii.gz")
)
else:
raise ValueError(f"Mask option '{mask}' not supported")
elif space == "mni152_2mm":
if mask is None:
img = nib.load(op.join(template_dir, "tpl-MNI152NLin6Asym_res-02_T1w.nii.gz"))
elif mask == "brain":
img = nib.load(
op.join(template_dir, "tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz")
)
else:
raise ValueError(f"Mask option '{mask}' not supported")
elif space == "ale_2mm":
if mask is None:
img = nib.load(op.join(template_dir, "tpl-MNI152NLin6Asym_res-02_T1w.nii.gz"))
elif mask == "brain":
# Not the same as the nilearn brain mask, but should correspond to
# the default "more conservative" MNI152 mask in GingerALE.
img = nib.load(op.join(template_dir, "MNI152_2x2x2_brainmask.nii.gz"))
else:
raise ValueError(f"Mask option '{mask}' not supported")
else:
raise ValueError(f"Space '{space}' not supported")
# Coerce to array-image
img = nib.Nifti1Image(img.get_fdata(), affine=img.affine, header=img.header)
return img
def get_masker(mask):
"""Get an initialized, fitted nilearn Masker instance from passed argument.
Parameters
----------
mask : str, :class:`nibabel.nifti1.Nifti1Image`, or any nilearn Masker
Returns
-------
masker : an initialized, fitted instance of a subclass of
`nilearn.input_data.base_masker.BaseMasker`
"""
if isinstance(mask, str):
mask = nib.load(mask)
if isinstance(mask, nib.nifti1.Nifti1Image):
# Coerce to array-image
mask = nib.Nifti1Image(mask.get_fdata(), affine=mask.affine, header=mask.header)
mask = NiftiMasker(mask)
if not (hasattr(mask, "transform") and hasattr(mask, "inverse_transform")):
raise ValueError(
"mask argument must be a string, a nibabel image, or a Nilearn Masker instance."
)
# Fit the masker if needed
if not hasattr(mask, "mask_img_"):
mask.fit()
return mask
def vox2mm(ijk, affine):
"""Convert matrix subscripts to coordinates.
.. versionchanged:: 0.0.8
* [ENH] This function was part of `nimare.transforms` in previous versions (0.0.3-0.0.7)
Parameters
----------
ijk : (X, 3) :obj:`numpy.ndarray`
Matrix subscripts for coordinates being transformed.
One row for each coordinate, with three columns: i, j, and k.
affine : (4, 4) :obj:`numpy.ndarray`
Affine matrix from image.
Returns
-------
xyz : (X, 3) :obj:`numpy.ndarray`
Coordinates in image-space.
Notes
-----
From here:
http://blog.chrisgorgolewski.org/2014/12/how-to-convert-between-voxel-and-mm.html
"""
xyz = nib.affines.apply_affine(affine, ijk)
return xyz
def mm2vox(xyz, affine):
"""Convert coordinates to matrix subscripts.
.. versionchanged:: 0.0.8
* [ENH] This function was part of `nimare.transforms` in previous versions (0.0.3-0.0.7)
Parameters
----------
xyz : (X, 3) :obj:`numpy.ndarray`
Coordinates in image-space.
One row for each coordinate, with three columns: x, y, and z.
affine : (4, 4) :obj:`numpy.ndarray`
Affine matrix from image.
Returns
-------
ijk : (X, 3) :obj:`numpy.ndarray`
Matrix subscripts for coordinates being transformed.
Notes
-----
From here:
http://blog.chrisgorgolewski.org/2014/12/how-to-convert-between-voxel-and-mm.html
"""
ijk = nib.affines.apply_affine(np.linalg.inv(affine), xyz).astype(int)
return ijk
def tal2mni(coords):
"""Convert coordinates from Talairach space to MNI space.
.. versionchanged:: 0.0.8
* [ENH] This function was part of `nimare.transforms` in previous versions (0.0.3-0.0.7)
Parameters
----------
coords : (X, 3) :obj:`numpy.ndarray`
Coordinates in Talairach space to convert.
Each row is a coordinate, with three columns.
Returns
-------
coords : (X, 3) :obj:`numpy.ndarray`
Coordinates in MNI space.
Each row is a coordinate, with three columns.
Notes
-----
Python version of BrainMap's tal2icbm_other.m.
This function converts coordinates from Talairach space to MNI
space (normalized using templates other than those contained
in SPM and FSL) using the tal2icbm transform developed and
validated by Jack Lancaster at the Research Imaging Center in
San Antonio, Texas.
http://www3.interscience.wiley.com/cgi-bin/abstract/114104479/ABSTRACT
"""
# Find which dimensions are of size 3
shape = np.array(coords.shape)
if all(shape == 3):
LGR.info("Input is an ambiguous 3x3 matrix.\nAssuming coords are row vectors (Nx3).")
use_dim = 1
elif not any(shape == 3):
raise AttributeError("Input must be an Nx3 or 3xN matrix.")
else:
use_dim = np.where(shape == 3)[0][0]
# Transpose if necessary
if use_dim == 1:
coords = coords.transpose()
# Transformation matrices, different for each software package
icbm_other = np.array(
[
[0.9357, 0.0029, -0.0072, -1.0423],
[-0.0065, 0.9396, -0.0726, -1.3940],
[0.0103, 0.0752, 0.8967, 3.6475],
[0.0000, 0.0000, 0.0000, 1.0000],
]
)
# Invert the transformation matrix
icbm_other = np.linalg.inv(icbm_other)
# Apply the transformation matrix
coords = np.concatenate((coords, np.ones((1, coords.shape[1]))))
coords = np.dot(icbm_other, coords)
# Format the output, transpose if necessary
out_coords = coords[:3, :]
if use_dim == 1:
out_coords = out_coords.transpose()
return out_coords
def mni2tal(coords):
"""Convert coordinates from MNI space Talairach space.
.. versionchanged:: 0.0.8
* [ENH] This function was part of `nimare.transforms` in previous versions (0.0.3-0.0.7)
Parameters
----------
coords : (X, 3) :obj:`numpy.ndarray`
Coordinates in MNI space to convert.
Each row is a coordinate, with three columns.
Returns
-------
coords : (X, 3) :obj:`numpy.ndarray`
Coordinates in Talairach space.
Each row is a coordinate, with three columns.
Notes
-----
Python version of BrainMap's icbm_other2tal.m.
This function converts coordinates from MNI space (normalized using
templates other than those contained in SPM and FSL) to Talairach space
using the icbm2tal transform developed and validated by Jack Lancaster at
the Research Imaging Center in San Antonio, Texas.
http://www3.interscience.wiley.com/cgi-bin/abstract/114104479/ABSTRACT
"""
# Find which dimensions are of size 3
shape = np.array(coords.shape)
if all(shape == 3):
LGR.info("Input is an ambiguous 3x3 matrix.\nAssuming coords are row vectors (Nx3).")
use_dim = 1
elif not any(shape == 3):
raise AttributeError("Input must be an Nx3 or 3xN matrix.")
else:
use_dim = np.where(shape == 3)[0][0]
# Transpose if necessary
if use_dim == 1:
coords = coords.transpose()
# Transformation matrices, different for each software package
icbm_other = np.array(
[
[0.9357, 0.0029, -0.0072, -1.0423],
[-0.0065, 0.9396, -0.0726, -1.3940],
[0.0103, 0.0752, 0.8967, 3.6475],
[0.0000, 0.0000, 0.0000, 1.0000],
]
)
# Apply the transformation matrix
coords = np.concatenate((coords, np.ones((1, coords.shape[1]))))
coords = np.dot(icbm_other, coords)
# Format the output, transpose if necessary
out_coords = coords[:3, :]
if use_dim == 1:
out_coords = out_coords.transpose()
return out_coords
def _dict_to_df(id_df, data, key="labels"):
"""Load a given data type in NIMADS-format dictionary into DataFrame.
Parameters
----------
id_df : :obj:`pandas.DataFrame`
DataFrame with columns for identifiers. Index is [studyid]-[expid].
data : :obj:`dict`
NIMADS-format dictionary storing the raw dataset, from which
relevant data are loaded into DataFrames.
key : {'labels', 'metadata', 'text', 'images'}
Which data type to load.
Returns
-------
df : :obj:`pandas.DataFrame`
DataFrame with id columns from id_df and new columns for the
requested data type.
"""
exp_dict = {}
for pid in data.keys():
for expid in data[pid]["contrasts"].keys():
exp = data[pid]["contrasts"][expid]
id_ = f"{pid}-{expid}"
if key not in data[pid]["contrasts"][expid].keys():
continue
exp_dict[id_] = exp[key]
temp_df = pd.DataFrame.from_dict(exp_dict, orient="index")
df = pd.merge(id_df, temp_df, left_index=True, right_index=True, how="outer")
df = df.reset_index(drop=True)
df = df.replace(to_replace="None", value=np.nan)
# replace nan with none
df = df.where(pd.notnull(df), None)
return df
def _dict_to_coordinates(data, masker, space):
"""Load coordinates in NIMADS-format dictionary into DataFrame."""
# Required columns
columns = ["id", "study_id", "contrast_id", "x", "y", "z", "space"]
core_columns = columns.copy() # Used in contrast for loop
all_dfs = []
for pid in data.keys():
for expid in data[pid]["contrasts"].keys():
if "coords" not in data[pid]["contrasts"][expid].keys():
continue
exp_columns = core_columns.copy()
exp = data[pid]["contrasts"][expid]
# Required info (ids, x, y, z, space)
n_coords = len(exp["coords"]["x"])
rep_id = np.array([[f"{pid}-{expid}", pid, expid]] * n_coords).T
space_arr = exp["coords"].get("space")
space_arr = np.array([space_arr] * n_coords)
temp_data = np.vstack(
(
rep_id,
np.array(exp["coords"]["x"]),
np.array(exp["coords"]["y"]),
np.array(exp["coords"]["z"]),
space_arr,
)
)
# Optional information
for k in list(set(exp["coords"].keys()) - set(core_columns)):
k_data = exp["coords"][k]
if not isinstance(k_data, list):
k_data = np.array([k_data] * n_coords)
exp_columns.append(k)
if k not in columns:
columns.append(k)
temp_data = np.vstack((temp_data, k_data))
# Place data in list of dataframes to merge
con_df = pd.DataFrame(temp_data.T, columns=exp_columns)
all_dfs.append(con_df)
if not all_dfs:
return pd.DataFrame(
{
"id": [],
"study_id": [],
"contrast_id": [],
"x": [],
"y": [],
"z": [],
"space": [],
},
)
df = pd.concat(all_dfs, axis=0, join="outer", sort=False)
df = df[columns].reset_index(drop=True)
df = df.replace(to_replace="None", value=np.nan)
# replace nan with none
df = df.where(pd.notnull(df), None)
df[["x", "y", "z"]] = df[["x", "y", "z"]].astype(float)
df = _transform_coordinates_to_space(df, masker, space)
return df
def _transform_coordinates_to_space(df, masker, space):
"""Convert xyz coordinates in a DataFrame to ijk indices for a given target space.
Parameters
----------
df : :obj:`pandas.DataFrame`
masker : :class:`~nilearn.input_data.NiftiMasker` or similar
Masker object defining the space and location of the area of interest
(e.g., 'brain').
space : :obj:`str`
String describing the stereotactic space and resolution of the masker.
Returns
-------
df : :obj:`pandas.DataFrame`
DataFrame with IJK columns either added or overwritten.
"""
# Now to apply transformations!
if "mni" in space.lower() or "ale" in space.lower():
transform = {"MNI": None, "TAL": tal2mni, "Talairach": tal2mni}
elif "tal" in space.lower():
transform = {"MNI": mni2tal, "TAL": None, "Talairach": None}
else:
raise ValueError(f"Unrecognized space: {space}")
found_spaces = df["space"].unique()
for found_space in found_spaces:
if found_space not in transform.keys():
LGR.warning(
f"Not applying transforms to coordinates in unrecognized space '{found_space}'"
)
alg = transform.get(found_space, None)
idx = df["space"] == found_space
if alg:
df.loc[idx, ["x", "y", "z"]] = alg(df.loc[idx, ["x", "y", "z"]].values)
df.loc[idx, "space"] = space
return df
def _validate_df(df):
"""Check that an input is a DataFrame and has a column for 'id'."""
assert isinstance(df, pd.DataFrame)
assert "id" in df.columns
def _validate_images_df(image_df):
"""Check and update image paths in DataFrame.
Parameters
----------
image_df : :class:`pandas.DataFrame`
DataFrame with one row for each study and one column for each image
type. Cells contain paths to image files.
Returns
-------
image_df : :class:`pandas.DataFrame`
DataFrame with updated paths and columns.
"""
valid_suffixes = [".brik", ".head", ".nii", ".img", ".hed"]
# Find columns in the DataFrame with images
file_cols = []
for col in image_df.columns:
vals = [v for v in image_df[col].values if isinstance(v, str)]
fc = any([any([vs in v for vs in valid_suffixes]) for v in vals])
if fc:
file_cols.append(col)
# Clean up DataFrame
# Find out which columns have full paths and which have relative paths
abs_cols = []
for col in file_cols:
files = image_df[col].tolist()
abspaths = [f == op.abspath(f) for f in files if isinstance(f, str)]
if all(abspaths):
abs_cols.append(col)
elif not any(abspaths):
if not col.endswith("__relative"):
image_df = image_df.rename(columns={col: col + "__relative"})
else:
raise ValueError(
f"Mix of absolute and relative paths detected for images in column '{col}'"
)
# Set relative paths from absolute ones
if len(abs_cols):
all_files = list(np.ravel(image_df[abs_cols].values))
all_files = [f for f in all_files if isinstance(f, str)]
if len(all_files) == 1:
# In the odd case where there's only one absolute path
shared_path = op.dirname(all_files[0]) + op.sep
else:
shared_path = _find_stem(all_files)
# Get parent *directory* if shared path includes common prefix.
if not shared_path.endswith(op.sep):
shared_path = op.dirname(shared_path) + op.sep
LGR.info(f"Shared path detected: '{shared_path}'")
image_df_out = image_df.copy() # To avoid SettingWithCopyWarning
for abs_col in abs_cols:
image_df_out[abs_col + "__relative"] = image_df[abs_col].apply(
lambda x: x.split(shared_path)[1] if isinstance(x, str) else x
)
image_df = image_df_out
return image_df
def _listify(obj):
"""Wrap all non-list or tuple objects in a list.
This provides a simple way to accept flexible arguments.
"""
return obj if isinstance(obj, (list, tuple, type(None), np.ndarray)) else [obj]
def _round2(ndarray):
"""Round X.5 to the nearest integer away from zero.
Numpy rounds X.5 values to nearest even integer.
"""
onedarray = ndarray.flatten()
signs = np.sign(onedarray) # pylint: disable=no-member
idx = np.where(np.abs(onedarray - np.round(onedarray)) == 0.5)[0]
x = np.abs(onedarray)
y = np.round(x)
y[idx] = np.ceil(x[idx])
y *= signs
rounded = y.reshape(ndarray.shape)
return rounded.astype(int)
def _try_prepend(value, prefix):
"""Try to prepend a value to a string with a separator ('/').
If not a string, will just return the original value.
"""
if isinstance(value, str):
return op.join(prefix, value)
else:
return value
def _find_stem(arr):
"""Find longest common substring in array of strings.
From https://www.geeksforgeeks.org/longest-common-substring-array-strings/
"""
# Determine size of the array
n_items_in_array = len(arr)
# Take first word from array as reference
reference_string = arr[0]
n_chars_in_first_item = len(reference_string)
res = ""
for i_char in range(n_chars_in_first_item):
# Generate all starting substrings of our reference string
stem = reference_string[:i_char]
j_item = 1 # Retained in case of an array with only one item
for j_item in range(1, n_items_in_array):
# Check if the generated stem is common to to all words
if not arr[j_item].startswith(stem):
break
# If current substring is present in all strings and its length is
# greater than current result
if (j_item + 1 == n_items_in_array) and (len(res) < len(stem)):
res = stem
return res
def _uk_to_us(text):
"""Convert UK spellings to US based on a converter.
.. versionadded:: 0.0.2
Parameters
----------
text : :obj:`str`
Returns
-------
text : :obj:`str`
Notes
-----
The english_spellings.csv file is from http://www.tysto.com/uk-us-spelling-list.html.
"""
SPELL_DF = pd.read_csv(op.join(get_resource_path(), "english_spellings.csv"), index_col="UK")
SPELL_DICT = SPELL_DF["US"].to_dict()
if isinstance(text, str):
# Convert British to American English
pattern = re.compile(r"\b(" + "|".join(SPELL_DICT.keys()) + r")\b")
text = pattern.sub(lambda x: SPELL_DICT[x.group()], text)
return text
def use_memmap(logger, n_files=1):
"""Memory-map array to a file, and perform cleanup after.
.. versionadded:: 0.0.8
Parameters
----------
logger : :obj:`logging.Logger`
A Logger with which to log information about the function.
n_files : :obj:`int`, optional
Number of memory-mapped files to create and manage.
Notes
-----
This function is used as a decorator to methods in which memory-mapped arrays may be used.
It will only be triggered if the class to which the method belongs has a ``memory_limit``
attribute that is set to something other than ``None``.
It will set an attribute within the method's class named ``memmap_filenames``, which is a list
of filename strings, with ``n_files`` elements.
If ``memory_limit`` is None, then it will be a list of ``Nones``.
Files generated by this function will be stored in the NiMARE data directory and will be
removed after the wrapped method finishes.
"""
def inner_function(function):
@wraps(function)
def memmap_context(self, *args, **kwargs):
if hasattr(self, "memory_limit") and self.memory_limit:
self.memmap_filenames, filenames = [], []
for i_file in range(n_files):
start_time = datetime.datetime.now().strftime("%Y%m%dT%H%M%S")
_, filename = mkstemp(prefix=self.__class__.__name__, suffix=start_time)
logger.debug(f"Temporary file written to {filename}")
self.memmap_filenames.append(filename)
filenames.append(filename)
else:
filenames = self.memmap_filenames = [None] * n_files
try:
return function(self, *args, **kwargs)
except:
for filename in filenames:
logger.error(f"{function.__name__} failed, removing {filename}")
raise
finally:
if hasattr(self, "memory_limit") and self.memory_limit:
for filename in filenames:
if os.path.isfile(filename):
logger.debug(f"Removing temporary file: {filename}")
os.remove(filename)
else:
logger.debug(f"Temporary file DNE: {filename}")
return memmap_context
return inner_function
BYTE = 2
KILOBYTE = BYTE**10
BYTE_CONVERSION = {
"kb": KILOBYTE,
"mb": KILOBYTE**2,
"gb": KILOBYTE**3,
"tb": KILOBYTE**4,
}
def _determine_chunk_size(limit, arr, multiplier=1):
"""Determine how many arrays can be read into memory at once.
Parameters
----------
limit : :obj:`str`
String representation of memory limit, can use:
kb, mb, gb, and tb as suffix (e.g., "4gb").
arr : :obj:`numpy.array`
Representative numpy array.
multiplier : :obj:`int`
Adjustment for processes that have more or
less overhead than expected.
"""
limit = limit.lower()
size, representation = re.search(r"([0-9]+)([a-z]+)", limit).groups()
limit_bytes = float(size) * BYTE_CONVERSION[representation] * multiplier
arr_bytes = arr.size * arr.itemsize
chunk_size = int(limit_bytes // arr_bytes)
if chunk_size == 0:
arr_size = arr_bytes // BYTE_CONVERSION["mb"]
raise RuntimeError(f"memory limit: {limit} too small for array with size {arr_size}mb")
return chunk_size
def _safe_transform(imgs, masker, memory_limit="1gb", dtype="auto", memfile=None):
"""Apply a masker with limited memory usage.
Parameters
----------
imgs : list of niimgs
List of images upon which to apply the masker.
masker : nilearn masker
Masker object to apply to images.
memory_limit : :obj:`str`, optional
String representation of memory limit, can use:
kb, mb, gb, and tb as suffix (e.g., "4gb").
dtype : :obj:`str`, optional
Target datatype of masked array.
Default is "auto", which uses the datatype of the niimgs.
memfile : :obj:`str` or None, optional
Name of a memory-mapped file. If None, memory-mapping will not be used.
Returns
-------
masked_data : :obj:`numpy.ndarray` or :obj:`numpy.memmap`
Masked data in a 2D array.
Either an ndarray (if memfile is None) or a memmap array (if memfile is a string).
"""
assert isinstance(memfile, (type(None), str))
first_img_data = masker.transform(imgs[0])
masked_shape = (len(imgs), first_img_data.size)
if memfile:
masked_data = np.memmap(
memfile,
dtype=first_img_data.dtype if dtype == "auto" else dtype,
mode="w+",
shape=masked_shape,
)
else:
masked_data = np.empty(
masked_shape,
dtype=first_img_data.dtype if dtype == "auto" else dtype,
)
# perform transform on chunks of the input maps
chunk_size = _determine_chunk_size(memory_limit, first_img_data)
map_chunks = [imgs[i : i + chunk_size] for i in range(0, len(imgs), chunk_size)]
idx = 0
for map_chunk in map_chunks:
end_idx = idx + len(map_chunk)
map_chunk_data = masker.transform(map_chunk)
masked_data[idx:end_idx, :] = map_chunk_data
idx = end_idx
return masked_data
def _add_metadata_to_dataframe(
dataset,
dataframe,
metadata_field,
target_column,
filter_func=np.mean,
):
"""Add metadata from a Dataset to a DataFrame.
.. versionadded:: 0.0.8
This is particularly useful for kernel transformers or estimators where a given metadata field
is necessary (e.g., ALEKernel with "sample_size"), but we want to just use the coordinates
DataFrame instead of passing the full Dataset.
Parameters
----------
dataset : :obj:`~nimare.dataset.Dataset`
Dataset containing study IDs and metadata to feed into dataframe.
dataframe : :obj:`pandas.DataFrame`
DataFrame containing study IDs, into which Dataset metadata will be merged.
metadata_field : :obj:`str`
Metadata field in ``dataset``.
target_column : :obj:`str`
Name of the column that will be added to ``dataframe``, containing information from the
Dataset.
filter_func : :obj:`function`, optional
Function to apply to the metadata so that it fits as a column in a DataFrame.
Default is ``numpy.mean``.
Returns
-------
dataframe : :obj:`pandas.DataFrame`
Updated DataFrame with ``target_column`` added.
"""
dataframe = dataframe.copy()
if metadata_field in dataset.get_metadata():
# Collect metadata from Dataset
metadata = dataset.get_metadata(field=metadata_field, ids=dataset.ids)
metadata = [[m] for m in metadata]
# Create a DataFrame with the metadata
metadata = pd.DataFrame(
index=dataset.ids,
data=metadata,
columns=[metadata_field],
)
# Reduce the metadata (if in list/array format) to single values
metadata[target_column] = metadata[metadata_field].apply(filter_func)
# Merge metadata df into coordinates df
dataframe = dataframe.merge(
right=metadata,
left_on="id",
right_index=True,
sort=False,
validate="many_to_one",
suffixes=(False, False),
how="left",
)
else:
LGR.warning(
f"Metadata field '{metadata_field}' not found. "
"Set a constant value for this field as an argument, if possible."
)
return dataframe
def _check_type(obj, clss, **kwargs):
"""Check variable type and initialize if necessary.
.. versionadded:: 0.0.8
Parameters
----------
obj
Object to check and initialized if necessary.
clss
Target class of the object.
kwargs
Dictionary of keyword arguments that can be used when initializing the object.
Returns
-------
obj
Initialized version of the object.
"""
# Allow both instances and classes for the input.
if not issubclass(type(obj), clss) and not issubclass(obj, clss):
raise ValueError(f"Argument {type(obj)} must be a kind of {clss}")
elif not inspect.isclass(obj) and kwargs:
LGR.warning(
f"Argument {type(obj)} has already been initialized, so arguments "
f"will be ignored: {', '.join(kwargs.keys())}"
)
elif inspect.isclass(obj):
obj = obj(**kwargs)
return obj
def _boolean_unmask(data_array, bool_array):
"""Unmask data based on a boolean array, with NaNs in empty voxels.
Parameters
----------
data_array : 1D or 2D :obj:`numpy.ndarray`
Masked data array.
bool_array : 1D :obj:`numpy.ndarray`
Boolean mask array. Must have the same number of ``True`` entries as elements in the
second dimension of ``data_array``.
Returns
-------
unmasked_data : 1D or 2D :obj:`numpy.ndarray`
Unmasked data array.
If 1D, first dimension is the same size as the first (and only) dimension of
``boolean_array``.
If 2D, first dimension is the same size as the first dimension of ``data_array``, while
second dimension is the same size as the first (and only) dimension of ``boolean_array``.
All elements corresponding to ``False`` values in ``boolean_array`` will have NaNs.
"""
assert data_array.ndim in (1, 2)
assert bool_array.ndim == 1
assert bool_array.sum() == data_array.shape[-1]
unmasked_data = np.full(
shape=bool_array.shape + data_array.T.shape[1:],
fill_value=np.nan,
dtype=data_array.dtype,
)
unmasked_data[bool_array] = data_array
unmasked_data = unmasked_data.T
return unmasked_data
@contextlib.contextmanager
def tqdm_joblib(tqdm_object):
"""Context manager to patch joblib to report into tqdm progress bar given as argument.
From https://stackoverflow.com/a/58936697/2589328.
"""
class TqdmBatchCompletionCallback(joblib.parallel.BatchCompletionCallBack):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
def __call__(self, *args, **kwargs):
tqdm_object.update(n=self.batch_size)
return super().__call__(*args, **kwargs)
old_batch_callback = joblib.parallel.BatchCompletionCallBack
joblib.parallel.BatchCompletionCallBack = TqdmBatchCompletionCallback
try:
yield tqdm_object
finally:
joblib.parallel.BatchCompletionCallBack = old_batch_callback
tqdm_object.close()
def unique_rows(ar, return_counts=False):
"""Remove repeated rows from a 2D array.
In particular, if given an array of coordinates of shape
(Npoints, Ndim), it will remove repeated points.
Parameters
----------
ar : 2-D ndarray
The input array.
return_counts : :obj:`bool`, optional
If True, also return the number of times each unique item appears in ar.
Returns
-------
ar_out : 2-D ndarray
A copy of the input array with repeated rows removed.
unique_counts : :obj:`np.ndarray`, optional
The number of times each of the unique values comes up in the original array.
Only provided if return_counts is True.
Raises
------
ValueError : if `ar` is not two-dimensional.