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Merge pull request #33 from yibeichan/wip-yc-convert
convert convertxfm.py
2 parents 58a272c + cca0b1f commit 6957eb6

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‎.gitattributes

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pydra/tasks/fsl/_version.py export-subst
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*.nii.gz filter=lfs diff=lfs merge=lfs -text
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*.nii* filter=lfs diff=lfs merge=lfs -text

‎.gitignore

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.DS_Store
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*/.DS_Store
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*/*/.DS_Store
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*/*/*/.DS_Store
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*/.DS_Store
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*/*/*/*/.DS_Store
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*/*/*/*/*/.DS_Store
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]

‎pydra/tasks/fsl/model/__init__.py

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‎pydra/tasks/fsl/model/cluster.py

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from pydra.engine import specs
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from pydra import ShellCommandTask
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import typing as ty
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def Cluster_output(inputs):
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import os, attr
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from pydra.engine.helpers_file import split_filename
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in_file = inputs.in_file
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pth, fname, ext = split_filename(in_file)
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return os.path.join(pth, f"{fname}_localmax.txt")
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input_fields = [
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(
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"in_file",
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specs.File,
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{"help_string": "input volume", "argstr": "--in={in_file}", "mandatory": True},
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),
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(
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"threshold",
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float,
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{
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"help_string": "threshold for input volume",
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"argstr": "--thresh={threshold:.10f}",
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"mandatory": True,
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},
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),
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(
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"out_index_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "output of cluster index (in size order)",
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"argstr": "--oindex={out_index_file}",
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"output_file_template": "{in_file}_index",
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},
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),
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(
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"out_threshold_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "thresholded image",
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"argstr": "--othresh={out_threshold_file}",
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"output_file_template": "{in_file}_threshold",
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},
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),
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(
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"out_localmax_txt_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "local maxima text file",
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"argstr": "--olmax={out_localmax_txt_file}",
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"output_file_template": Cluster_output,
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},
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),
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(
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"out_localmax_vol_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "output of local maxima volume",
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"argstr": "--olmaxim={out_localmax_vol_file}",
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"output_file_template": "{in_file}_localmax",
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},
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),
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(
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"out_size_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "filename for output of size image",
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"argstr": "--osize={out_size_file}",
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"output_file_template": "{in_file}_size",
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},
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),
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(
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"out_max_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "filename for output of max image",
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"argstr": "--omax={out_max_file}",
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"output_file_template": "{in_file}_max",
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},
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),
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(
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"out_mean_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "filename for output of mean image",
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"argstr": "--omean={out_mean_file}",
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"output_file_template": "{in_file}_mean",
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},
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),
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(
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"out_pval_file",
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ty.Union[bool, str],
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False,
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{
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"help_string": "filename for image output of log pvals",
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"argstr": "--opvals={out_pval_file}",
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"output_file_template": "{in_file}_pval",
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},
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),
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(
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"pthreshold",
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float,
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{
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"help_string": "p-threshold for clusters",
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"argstr": "--pthresh={pthreshold:.10f}",
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"requires": ["dlh", "volume"],
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},
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),
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(
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"peak_distance",
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float,
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{
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"help_string": "minimum distance between local maxima/minima, in mm (default 0)",
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"argstr": "--peakdist={peak_distance:.10f}",
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},
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),
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("cope_file", str, {"help_string": "cope volume", "argstr": "--cope={cope_file}"}),
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(
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"volume",
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int,
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{"help_string": "number of voxels in the mask", "argstr": "--volume={volume}"},
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),
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(
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"dlh",
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float,
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{
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"help_string": "smoothness estimate = sqrt(det(Lambda))",
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"argstr": "--dlh={dlh:.10f}",
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},
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),
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(
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"fractional",
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bool,
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False,
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{
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"help_string": "interprets the threshold as a fraction of the robust range",
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"argstr": "--fractional",
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},
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),
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(
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"connectivity",
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int,
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{
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"help_string": "the connectivity of voxels (default 26)",
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"argstr": "--connectivity={connectivity}",
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},
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),
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(
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"use_mm",
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bool,
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False,
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{"help_string": "use mm, not voxel, coordinates", "argstr": "--mm"},
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),
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(
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"find_min",
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bool,
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False,
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{"help_string": "find minima instead of maxima", "argstr": "--min"},
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),
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(
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"no_table",
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bool,
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False,
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{
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"help_string": "suppresses printing of the table info",
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"argstr": "--no_table",
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},
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),
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(
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"minclustersize",
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bool,
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False,
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{
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"help_string": "prints out minimum significant cluster size",
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"argstr": "--minclustersize",
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},
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),
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(
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"xfm_file",
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str,
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{
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"help_string": "filename for Linear: input->standard-space transform. Non-linear: input->highres transform",
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"argstr": "--xfm={xfm_file}",
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},
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),
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(
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"std_space_file",
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str,
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{
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"help_string": "filename for standard-space volume",
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"argstr": "--stdvol={std_space_file}",
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},
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),
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(
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"num_maxima",
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int,
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{"help_string": "no of local maxima to report", "argstr": "--num={num_maxima}"},
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),
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(
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"warpfield_file",
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str,
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{
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"help_string": "file contining warpfield",
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"argstr": "--warpvol={warpfield_file}",
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},
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),
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]
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Cluster_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = []
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Cluster_output_spec = specs.SpecInfo(
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name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
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)
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class Cluster(ShellCommandTask):
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"""
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Example
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-------
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>>> task = Cluster()
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>>> task.inputs.in_file = "zstat1.nii.gz"
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>>> task.inputs.out_localmax_txt_file = True
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>>> task.inputs.threshold = 2.3
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>>> task.inputs.use_mm = True
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>>> task.cmdline
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'cluster --in=zstat1.nii.gz --olmax=zstat1_localmax.txt --thresh=2.3000000000 --mm'
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"""
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input_spec = Cluster_input_spec
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output_spec = Cluster_output_spec
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executable = "cluster"

‎pydra/tasks/fsl/model/feat.py

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from pydra.engine import specs
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from pydra import ShellCommandTask
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import typing as ty
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def FEAT_output(fsf_file):
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is_ica = False
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with open(fsf_file, "rt") as fp:
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text = fp.read()
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if "set fmri(inmelodic) 1" in text:
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is_ica = True
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for line in text.split("\n"):
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if line.find("set fmri(outputdir)") > -1:
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try:
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outputdir_spec = line.split('"')[-2]
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if os.path.exists(outputdir_spec):
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outputs = outputdir_spec
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except:
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pass
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if not outputs:
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if is_ica:
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outputs = glob(os.path.join(os.getcwd(), "*ica"))[0]
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else:
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outputs = glob(os.path.join(os.getcwd(), "*feat"))[0]
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print("Outputs from FEATmodel:", outputs)
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return outputs
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input_fields = [
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(
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"fsf_file",
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specs.File,
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{
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"help_string": "File specifying the feat design spec file",
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"argstr": "{fsf_file}",
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"mandatory": True,
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"position": 0,
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},
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)
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]
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FEAT_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = [
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("feat_dir", specs.Directory, {"requires": ["fsf_file"], "callable": FEAT_output})
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]
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FEAT_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
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class FEAT(ShellCommandTask):
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"""
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Example
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-------
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>>> task = FEAT()
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>>> task.inputs.fsf_file = "test.fsf"
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>>> task.cmdline
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'feat test.fsf'
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"""
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input_spec = FEAT_input_spec
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output_spec = FEAT_output_spec
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executable = "feat"

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