neurosynth/base/dataset.py
def get_image_data(self, ids=None, voxels=None, dense=True):
        """ Slices and returns a subset of image data.

        Args:
            ids (list, array): A list or 1D numpy array of study ids to
                return. If None, returns data for all studies.
            voxels (list, array): A list or 1D numpy array of voxel indices
                (i.e., rows) to return. If None, returns data for all voxels.
            dense (bool): Optional boolean. When True (default), convert the
                result to a dense array before returning. When False, keep as
                sparse matrix.

        Returns:
          A 2D numpy array with voxels in rows and studies in columns.
        """
        if dense and ids is None and voxels is None:
            logger.warning(
                "Warning: get_image_data() is being called without specifying "
                "a subset of studies or voxels to retrieve. This may result in"
                " a very large amount of data (several GB) being read into "
                "memory. If you experience any problems, consider returning a "
                "sparse matrix by passing dense=False, or pass in a list of "
                "ids of voxels to retrieve only a portion of the data.")

        result = self.data
        if ids is not None:
            idxs = np.where(np.in1d(np.array(self.ids), np.array(ids)))[0]
            result = result[:, idxs]
        if voxels is not None:
            result = result[voxels, :]
        return result.toarray() if dense else result
def get_image_data(self, ids=None, voxels=None, dense=True):
        """ Slices and returns a subset of image data.

        Args:
            ids (list, array): A list or 1D numpy array of study ids to
                return. If None, returns data for all studies.
            voxels (list, array): A list or 1D numpy array of voxel indices
                (i.e., rows) to return. If None, returns data for all voxels.
            dense (bool): Optional boolean. When True (default), convert the
                result to a dense array before returning. When False, keep as
                sparse matrix.

        Returns:
          A 2D numpy array with voxels in rows and studies in columns.
        """
        if dense and ids is None and voxels is None:
            logger.warning(
                "Warning: get_image_data() is being called without specifying "
                "a subset of studies or voxels to retrieve. This may result in"
                " a very large amount of data (several GB) being read into "
                "memory. If you experience any problems, consider returning a "
                "sparse matrix by passing dense=False, or pass in a list of "
                "ids of voxels to retrieve only a portion of the data.")

        result = self.data
        if ids is not None:
            idxs = np.where(np.in1d(np.array(self.ids), np.array(ids)))[0]
            result = result[:, idxs]
        if voxels is not None:
            result = result[voxels, :]
        return result.toarray() if dense else result
Slices and returns a subset of image data.

        Args:
            ids (list, array): A list or 1D numpy array of study ids to
                return. If None, returns data for all studies.
            voxels (list, array): A list or 1D numpy array of voxel indices
                (i.e., rows) to return. If None, returns data for all voxels.
            dense (bool): Optional boolean. When True (default), convert the
                result to a dense array before returning. When False, keep as
                sparse matrix.

        Returns:
          A 2D numpy array with voxels in rows and studies in columns.