diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f7c3ee03..5126ae0cf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## Version 0.7.0 (September, 2018) +## Version 0.7.0 (January 10, 2019) This is a major, API-breaking release. It introduces a large number of new features, bug fixes, and improvements. API-BREAKING CHANGES: @@ -14,20 +14,36 @@ API-BREAKING CHANGES: * The BIDS validator is now enabled by default at layout initialization (i.e., `validate=True`) * The `exclude` initialization argument has been removed. * `BIDSLayout.parse_entities` utility has been removed (use the more flexible `parse_file_entities`). +* Calls to `.get()` now return `BIDSFile` objects, rather than namedtuples, by default (#281). The `BIDSFile` API has been tweaked to ensure backwards incompatibility in nearly all cases. +* Naming conventions throughout the codebase have been updated to ensure consistency with the BIDS specs. This is most salient in the `analysis` module, where snake_case has been replaced with CamelCase throughout. NEW FEATURES: -* File metadata is now searchable (use `BIDSLayout.search_metadata()`) +* File metadata (i.e., in JSON sidecars) is now searchable by default, and behaves just like native BIDS entities (e.g., metadata keys can be passed as arguments to `.get()` calls) * A new BIDSFile wrapper provides easy access to `.metadata` and `.image` * HRF convolution is now supported via bundling of nistats' hemodynamic_models module; convolution is handled via the `convolve_HRF` transformation. +* Named config paths that customize how projects are processed can be added at run-time (#313) +* Preliminary support for BIDS-Derivatives RC1 (mainly core keywords) MINOR IMPROVEMENTS AND BUG FIXES: -* Specifying 'derivatives' in a paths specification now automatically includes 'bids' (#246) +* Specifying 'derivatives' in a path specification now automatically includes 'bids' (#246) +* Zenodo DOIs are now minted with new releases (#308) * Variable loading via load_variables can now be done incrementally * Expanded and improved path-building via `layout.build_path()` * `get_collections` no longer breaks when `merge=True` and the list is empty (#202) * Layout initialization no longer fails when `validate=True` (#222) * The auto_contrasts field in the modeling tools now complies with the BIDS-Model spec (#234) -* Fix sum transformation +* Printing a `BIDSFile` now provides more useful information, including path (#298) +* Resample design matrix to 1/TR by default (#309) +* Fix the Sum transformation +* Ensure that resampling works properly when a sampling rate is passed to `get_design_matrix` (#297) +* Propagate derivative entities into top-level dynamic getters (#306) +* Deprecated `get_header` call in nibabel removed (#300) +* Fix bug in entity indexing for `BIDSVariableCollection` (#319) +* Exclude modules with heavy dependencies from root namespace for performance reasons (#321) +* Fix bug that caused in-place updating of input selectors in `Analysis` objects (#323) +* Add a DropNA transformation (#325) +* Add a `get_tr()` method to `BIDSLayout` (#327) +* Add entity hints when calling `get()` with a `target` argument (#328) * Improved test coverage ## Version 0.6.5 (August 21, 2018) diff --git a/bids/layout/config/bids.json b/bids/layout/config/bids.json index 6d1052421..b70f08b56 100644 --- a/bids/layout/config/bids.json +++ b/bids/layout/config/bids.json @@ -4,13 +4,13 @@ { "name": "subject", "pattern": "[/\\\\]sub-([a-zA-Z0-9]+)", - "directory": "{{root}}/{subject}" + "directory": "{{root}}{subject}" }, { "name": "session", "pattern": "[_/\\\\]ses-([a-zA-Z0-9]+)", "mandatory": false, - "directory": "{{root}}/{subject}/{session}", + "directory": "{{root}}{subject}{session}", "missing_value": "ses-1" }, { diff --git a/bids/layout/layout.py b/bids/layout/layout.py index 8c61d51cd..0a539a7d7 100644 --- a/bids/layout/layout.py +++ b/bids/layout/layout.py @@ -377,6 +377,11 @@ def get(self, return_type='object', target=None, extensions=None, (see return_type for details). """ + # Warn users still expecting 0.6 behavior + if 'type' in kwargs: + raise ValueError("As of pybids 0.7.0, the 'type' argument has been" + " replaced with 'suffix'.") + if derivatives is True: derivatives = list(self.derivatives.keys()) elif derivatives: @@ -414,8 +419,9 @@ def get(self, return_type='object', target=None, extensions=None, # Get entity-based search results using the superclass's get() result = [] result = super( - BIDSLayout, self).get(return_type, target, extensions, None, - regex_search, **ent_kwargs) + BIDSLayout, self).get(return_type, target=target, + extensions=extensions, domains=None, + regex_search=regex_search, **ent_kwargs) # Search the metadata if needed if return_type not in {'dir', 'id'}: diff --git a/examples/pybids tutorial.ipynb b/examples/pybids tutorial.ipynb index e5d976536..0e115da44 100644 --- a/examples/pybids tutorial.ipynb +++ b/examples/pybids tutorial.ipynb @@ -22,8 +22,8 @@ }, "outputs": [], "source": [ - "import bids.layout\n", - "import bids.tests\n", + "from bids import BIDSLayout, BIDSValidator\n", + "from bids.tests import get_test_data_path\n", "import os" ] }, @@ -59,8 +59,8 @@ ], "source": [ "# Initialise a BIDSLayout of an example dataset\n", - "data_path = os.path.join(bids.tests.get_test_data_path(), '7t_trt')\n", - "layout = bids.layout.BIDSLayout(data_path)\n", + "data_path = os.path.join(get_test_data_path(), '7t_trt')\n", + "layout = BIDSLayout(data_path)\n", "layout" ] }, @@ -68,8 +68,8 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Using `get()`\n", - "a `BIDSLayout` object can be queried with the class method [`get()`](https://bids-standard.github.io/pybids/generated/bids.grabbids.BIDSLayout.html#bids.grabbids.BIDSLayout.get). The `BIDSLayout` object contains `File` objects. We can see the whole list of these by calling `get()` with no arguments" + "### Querying and working with `BIDSFile` objects\n", + "a `BIDSLayout` object can be queried with the class method [`get()`](https://bids-standard.github.io/pybids/generated/bids.grabbids.BIDSLayout.html#bids.grabbids.BIDSLayout.get). The `BIDSLayout` object contains `BIDSFile` objects. We can see the whole list of these by calling `get()` with no arguments:" ] }, { @@ -86,7 +86,7 @@ { "data": { "text/plain": [ - "File(filename='/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.json', subject='01', session='1', run=2, suffix='phasediff', datatype='fmap')" + "" ] }, "execution_count": 3, @@ -95,7 +95,7 @@ } ], "source": [ - "# The file objects returned are tuples of key-value pairs\n", + "# Print a summary of the 10th BIDSFile in the list\n", "layout.get()[10]" ] }, @@ -103,24 +103,32 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "`get()` returns (by default) a key-value pair tuple view of the matched file objects. We can match on these key value pairs." + "A `BIDSFile` has various attributes we might be interested in:\n", + "* `.path`: The full path of the associated file\n", + "* `.filename`: The associated file's filename (without directory)\n", + "* `.dirname`: The directory containing the file\n", + "* `.image`: The file contents as a nibabel image, if the file is an image\n", + "* `.metadata`: A dictionary of all metadata found in associated JSON files\n", + "* `entities`: A dictionary of BIDS entities (or keywords) extracted from the filename\n", + "\n", + "For example, here's the `dict` of entities for the 10th file in our list:" ] }, { "cell_type": "code", "execution_count": 4, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.933121Z", - "start_time": "2018-08-01T20:05:23.927623Z" - }, - "scrolled": true - }, + "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[File(filename='/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz', subject='01', session='1', suffix='T1w', datatype='anat')]" + "{'subject': '08',\n", + " 'session': '2',\n", + " 'task': 'rest',\n", + " 'acquisition': 'fullbrain',\n", + " 'run': 1,\n", + " 'suffix': 'physio',\n", + " 'datatype': 'func'}" ] }, "execution_count": 4, @@ -129,40 +137,28 @@ } ], "source": [ - "# We query for any files with the type 'T1w' \n", - "layout.get(suffix='T1w', subject='01')" + "f = layout.get()[10]\n", + "f.entities" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "[`get()`](https://bids-standard.github.io/pybids/generated/bids.grabbids.BIDSLayout.html#bids.grabbids.BIDSLayout.get) has been returning a \"tuple\" representation of the `File` objects, but we can specify the return type using optional argument `return_type`" + "And here's the metadata:" ] }, { "cell_type": "code", "execution_count": 5, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.945162Z", - "start_time": "2018-08-01T20:05:23.934513Z" - } - }, + "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[,\n", - " ,\n", - " ,\n", - " ,\n", - " ,\n", - " ,\n", - " ,\n", - " ,\n", - " ,\n", - " ]" + "{'StartTime': 0,\n", + " 'SamplingFrequency': 100,\n", + " 'Columns': ['cardiac', 'respiratory', 'trigger', 'oxygen saturation']}" ] }, "execution_count": 5, @@ -171,60 +167,23 @@ } ], "source": [ - "# Ask get() to return the matching file objects\n", - "layout.get(suffix='T1w', return_type='obj')\n", - "# You can convert an obj to a tuple by using the .as_named_tuple() method" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.954948Z", - "start_time": "2018-08-01T20:05:23.947869Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "['/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-02/ses-1/anat/sub-02_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-03/ses-1/anat/sub-03_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-04/ses-1/anat/sub-04_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-05/ses-1/anat/sub-05_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-06/ses-1/anat/sub-06_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-07/ses-1/anat/sub-07_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-08/ses-1/anat/sub-08_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-09/ses-1/anat/sub-09_ses-1_T1w.nii.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-10/ses-1/anat/sub-10_ses-1_T1w.nii.gz']" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Ask get() to return the filenames of the matching files\n", - "layout.get(suffix='T1w', return_type='file')" + "f.metadata" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "We can also ask get to return other key/value data from the `File` objects using the argument `target`" + "The entity and metadata dictionaries aren't just there for our casual perusal once we've already retrieved a `BIDSFile`; we can directly filter files from the `BIDSLayout` by requesting only files that match specific values. Some examples:" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.964766Z", - "start_time": "2018-08-01T20:05:23.957477Z" + "end_time": "2018-08-01T20:05:23.933121Z", + "start_time": "2018-08-01T20:05:23.927623Z" }, "scrolled": true }, @@ -232,372 +191,297 @@ { "data": { "text/plain": [ - "['01', '02', '03', '04', '05', '06', '07', '08', '09', '10']" + "[]" ] }, - "execution_count": 7, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# Ask get() to return the ids of subjects that have T1w files\n", - "layout.get(suffix='T1w', return_type='id', target='subject')" + "# We query for any files with the suffix 'T1w', only for subject '01'\n", + "layout.get(suffix='T1w', subject='01')" ] }, { "cell_type": "code", - "execution_count": 8, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.973072Z", - "start_time": "2018-08-01T20:05:23.967232Z" - } - }, + "execution_count": 7, + "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['anat', 'fmap', 'func']" + "[,\n", + " ,\n", + " ,\n", + " ]" ] }, - "execution_count": 8, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# See all modality labels in this dataset\n", - "layout.get(return_type='id', target='datatype')" + "# Retrieve all files where SamplingFrequency (a metadata key) = 100\n", + "# and acquisition = prefrontal, for the first two subjects\n", + "layout.get(subject=['01', '02'], SamplingFrequency=100, acquisition=\"prefrontal\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "And if our `target` is a key that corresponds to a particular directory in the BIDS spec (e.g subject or session) we can ask get to return the `target` subdirectory for each matching file." + "By default, [`get()`](https://bids-standard.github.io/pybids/generated/bids.grabbids.BIDSLayout.html#bids.grabbids.BIDSLayout.get) returns a `BIDSFile` object, but we can also specify alternative return types using the `return_type` argument. Here, we return only the full filenames as strings:" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.983125Z", - "start_time": "2018-08-01T20:05:23.975085Z" + "end_time": "2018-08-01T20:05:23.954948Z", + "start_time": "2018-08-01T20:05:23.947869Z" } }, "outputs": [ { "data": { "text/plain": [ - "[File(filename='/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz', subject='01', session='1', suffix='T1map', datatype='anat'),\n", - " File(filename='/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz', subject='01', session='1', suffix='T1w', datatype='anat')]" + "['/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-02/ses-1/anat/sub-02_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-03/ses-1/anat/sub-03_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-04/ses-1/anat/sub-04_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-05/ses-1/anat/sub-05_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-06/ses-1/anat/sub-06_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-07/ses-1/anat/sub-07_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-08/ses-1/anat/sub-08_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-09/ses-1/anat/sub-09_ses-1_T1w.nii.gz',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-10/ses-1/anat/sub-10_ses-1_T1w.nii.gz']" ] }, - "execution_count": 9, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# We can feed get more complicated queries\n", - "layout.get(suffix=['T1w', 'T1map'], subject='01')" + "# Ask get() to return the filenames of the matching files\n", + "layout.get(suffix='T1w', return_type='file')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can also ask `get()` to return unique values (or ids) of particular entities. For example, say we want to know which subjects have at least one `T1w` file. We can request that information by setting `return_type='id'` and `target='subject'`:" ] }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 9, "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:23.991504Z", - "start_time": "2018-08-01T20:05:23.985349Z" - } + "end_time": "2018-08-01T20:05:23.964766Z", + "start_time": "2018-08-01T20:05:23.957477Z" + }, + "scrolled": true }, "outputs": [ { "data": { "text/plain": [ - "['bold', 'description', 'phasediff', 'physio']" + "['08', '01', '07', '09', '10', '05', '06', '02', '04', '03']" ] }, - "execution_count": 10, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# See all the type values for json files in this dataset\n", - "layout.get(return_type='id', target='suffix', extensions='.json')" + "# Ask get() to return the ids of subjects that have T1w files\n", + "layout.get(suffix='T1w', return_type='id', target='subject')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "### What can we do with `File` objects?" + "If our `target` is a BIDS entity that corresponds to a particular directory in the BIDS spec (e.g., `subject` or `session`) we can also use `return_type='dir'` to get all matching subdirectories:" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 10, "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.002161Z", - "start_time": "2018-08-01T20:05:23.993809Z" + "end_time": "2018-08-01T20:05:23.983125Z", + "start_time": "2018-08-01T20:05:23.975085Z" } }, "outputs": [ { "data": { "text/plain": [ - "File(filename='/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.nii.gz', subject='01', session='1', run=1, suffix='phasediff', fmap='phasediff', datatype='fmap')" + "['/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-08',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-05',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-09',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-02',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-03',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-07',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-01',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-04',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-06',\n", + " '/Users/tal/Dropbox/Code/pybids/bids/tests/data/7t_trt/sub-10']" ] }, - "execution_count": 11, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# We can convert File objects into a named tuple \n", - "f = layout.get(return_type='obj', subject='01', session='1', run='1', suffix='phasediff', datatype='fmap')[1]\n", - "f.as_named_tuple()" + "layout.get(return_type='dir', target='subject')" ] }, { - "cell_type": "code", - "execution_count": 12, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.011465Z", - "start_time": "2018-08-01T20:05:24.004234Z" - }, - "scrolled": true - }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'EchoTime1': 0.006,\n", - " 'EchoTime2': 0.00702,\n", - " 'IntendedFor': 'ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz'}" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "cell_type": "markdown", + "metadata": {}, "source": [ - "# get_metadata reads the associated json file\n", - "layout.get_metadata(f.path)" + "## Other utilities" ] }, { - "cell_type": "code", - "execution_count": 13, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.020395Z", - "start_time": "2018-08-01T20:05:24.013878Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'datatype': 'fmap',\n", - " 'filename': '/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.nii.gz',\n", - " 'fmap': 'phasediff',\n", - " 'run': 1,\n", - " 'session': '1',\n", - " 'subject': '01',\n", - " 'suffix': 'phasediff'}" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "cell_type": "markdown", + "metadata": {}, "source": [ - "# Get file object as a dictionary\n", - "dict(f.as_named_tuple()._asdict())" + "Say you have a filename, and you want to manually extract BIDS entities from it. The `parse_file_entities` method provides the facility:" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 11, "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.027594Z", - "start_time": "2018-08-01T20:05:24.022698Z" + "end_time": "2018-08-01T20:05:24.035216Z", + "start_time": "2018-08-01T20:05:24.030080Z" } }, "outputs": [ { "data": { "text/plain": [ - "{'datatype': 'fmap',\n", - " 'fmap': 'phasediff',\n", - " 'run': 1,\n", - " 'session': '1',\n", - " 'subject': '01',\n", - " 'suffix': 'phasediff'}" + "{'subject': '01', 'run': 1, 'suffix': 'T2w'}" ] }, - "execution_count": 14, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# We can return file key value pairs as dictionaries\n", - "f.entities" + "path = \"/a/fake/path/to/a/BIDS/file/sub-01_run-1_T2w.nii.gz\"\n", + "layout.parse_file_entities(path)" ] }, { - "cell_type": "code", - "execution_count": 15, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.035216Z", - "start_time": "2018-08-01T20:05:24.030080Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'datatype': 'fmap',\n", - " 'fmap': 'phasediff',\n", - " 'run': 1,\n", - " 'session': '1',\n", - " 'subject': '01',\n", - " 'suffix': 'phasediff'}" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], + "cell_type": "markdown", + "metadata": {}, "source": [ - "# Layout can parse filenames to create this same dictionary of entities\n", - "layout.parse_file_entities(f.path)" + "You may want to create valid BIDS filenames for files that are new or hypothetical that would sit within your BIDS project. This is useful when you know what entity values you need to write out to, but don't want to deal with looking up the precise BIDS file-naming syntax. In the example below, imagine we've created a new file containing stimulus presentation information, and we want to save it to a `.tsv.gz` file, per the BIDS naming conventions. All we need to do is define a dictionary with the name components, and `build_path` takes care of the rest (including injecting sub-directories!):" ] }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 12, "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.042481Z", - "start_time": "2018-08-01T20:05:24.037268Z" + "end_time": "2018-08-01T20:05:24.049418Z", + "start_time": "2018-08-01T20:05:24.044544Z" } }, "outputs": [ { "data": { "text/plain": [ - "{'session': '1', 'subject': '02', 'suffix': 'T2w'}" + "'sub-01/func/sub-01_task-n-back_run-2_stim.tsv.gz'" ] }, - "execution_count": 16, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# We can even make up a filename and ask layout to parse it \n", - "layout.parse_file_entities(os.path.join(data_path, 'sub-02/ses-1/sub-02_ses-1_T2w.nii.gz'))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Build New Paths\n", + "entities = {\n", + " 'subject': '01',\n", + " 'run': 2,\n", + " 'task': 'n-back',\n", + " 'extension': 'tsv.gz',\n", + " 'suffix': 'stim'\n", + "}\n", "\n", - "You may want to create valid BIDS filenames for files that are new or hypothetical that would sit within your BIDS project. " + "layout.build_path(entities)" ] }, { - "cell_type": "code", - "execution_count": 17, + "cell_type": "markdown", "metadata": { "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.049418Z", - "start_time": "2018-08-01T20:05:24.044544Z" - } + "end_time": "2018-08-01T20:05:24.064220Z", + "start_time": "2018-08-01T20:05:24.058906Z" + }, + "scrolled": false }, - "outputs": [], "source": [ - "# You need to define a pattern for filenames. This is a string object with \n", - "# replaceable keys in curly brackets\n", - "pattern = \"sub-{subject}[/ses-{session}]/{modality}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{type}.nii.gz\"\n", - "# And you need to make a dictionary of entities. These are the key-value pairs that will \n", - "# define how to replace the {key}s in the pattern\n", - "entities = {'subject': '01', 'session': '1', 'modality': 'anat', 'type': 'T1w' }" + "You can also use `build_path` in more sophisticated ways—for example, by defining your own set of matching templates that cover cases not supported by BIDS out of the box. For example, suppose you want to create a template for naming a new z-stat file. You could do something like:" ] }, { "cell_type": "code", - "execution_count": 18, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.056894Z", - "start_time": "2018-08-01T20:05:24.051892Z" - } - }, + "execution_count": 13, + "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "'sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz'" + "'sub-01_task-n-back_run-2_z.nii.gz'" ] }, - "execution_count": 18, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# You can pass patterns directly to build_path\n", - "layout.build_path(entities, path_patterns=[pattern])" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": { - "ExecuteTime": { - "end_time": "2018-08-01T20:05:24.064220Z", - "start_time": "2018-08-01T20:05:24.058906Z" - }, - "scrolled": false - }, - "outputs": [], - "source": [ - "# Or you can define the default patterns for layout to use\n", - "# TODO: fix for 0.7 release\n", - "layout.path_patterns = [pattern]\n", - "layout.build_path(entities)" + "# Define the pattern to build out of the components passed in the dictionary\n", + "pattern = \"sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix}.nii.gz\",\n", + "\n", + "entities = {\n", + " 'subject': '01',\n", + " 'run': 2,\n", + " 'task': 'n-back',\n", + " 'suffix': 'z'\n", + "}\n", + "\n", + "# Notice we pass the new pattern as the second argument\n", + "layout.build_path(entities, pattern)\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "### Loading subdomains\n", + "### Loading derivatives\n", "\n", - "You can declare your `derivatives` subfolder when you initialise your `BIDSLayout`. This will endow it with the extra structure specified in the [derivatives config file](https://github.com/bids-standard/pybids/blob/master/bids/grabbids/config/derivatives.json)." + "By default, `BIDSLayout` objects are initialized without scanning contained `derivatives/` directories. But you can easily ensure that all derivatives files are loaded and endowed with the extra structure specified in the [derivatives config file](https://github.com/bids-standard/pybids/blob/master/bids/grabbids/config/derivatives.json):" ] }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 14, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:24.228683Z", @@ -606,25 +490,26 @@ }, "outputs": [ { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/yoh/proj/bids/pybids/venvs/dev3/lib/python3.6/site-packages/grabbit/core.py:448: UserWarning: Domain with name 'bids' already exists; returning existing Domain configuration.\n", - " warnings.warn(msg)\n" - ] + "data": { + "text/plain": [ + "BIDS Layout: ...bids/bids/tests/data/synthetic | Subjects: 5 | Sessions: 10 | Runs: 10" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ "# Define paths to root and derivatives folders\n", - "root = os.path.join(bids.tests.get_test_data_path(), 'synthetic')\n", - "# deriv = os.path.join(root, 'derivatives')\n", - "# import root as a 'bids' domain, and derivatives as a 'bids' and 'derivatives' domain\n", - "layout2 = bids.layout.BIDSLayout(root, derivatives=True)" + "root = os.path.join(get_test_data_path(), 'synthetic')\n", + "layout2 = BIDSLayout(root, derivatives=True)\n", + "layout2" ] }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 15, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:24.245649Z", @@ -636,281 +521,436 @@ { "data": { "text/plain": [ - "['/home/yoh/proj/bids/pybids/bids/tests/data/synthetic/derivatives/fmriprep/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-01_confounds.tsv.gz',\n", - " '/home/yoh/proj/bids/pybids/bids/tests/data/synthetic/derivatives/fmriprep/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-01_desc-preproc_space-MNI152NLin2009cAsym_bold.nii',\n", - " 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NaN\n", - " NaN\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", + " fmap\n", + " magnitude1\n", + " 1.0\n", " NaN\n", + " 2\n", " 08\n", - " sessions\n", + " magnitude1\n", " NaN\n", " \n", " \n", " 1\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", + " NaN\n", + " fmap\n", " NaN\n", " 2.0\n", " NaN\n", " 2\n", " 08\n", - " bold\n", - " rest\n", + " phasediff\n", + " NaN\n", " \n", " \n", " 2\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", - " 2.0\n", + " fmap\n", + " phasediff\n", + " 1.0\n", " NaN\n", " 2\n", " 08\n", - " physio\n", - " rest\n", + " phasediff\n", + " NaN\n", " \n", " \n", " 3\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", - " 1.0\n", + " fmap\n", + " magnitude1\n", + " 2.0\n", " NaN\n", " 2\n", " 08\n", - " bold\n", - " rest\n", + " magnitude1\n", + " NaN\n", " \n", " \n", " 4\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " prefrontal\n", - " func\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", + " fmap\n", " NaN\n", + " 1.0\n", " NaN\n", " 2\n", " 08\n", - " bold\n", - " rest\n", + " phasediff\n", + " NaN\n", " \n", " \n", "\n", @@ -1044,21 +1084,21 @@ ], "text/plain": [ " path acquisition datatype \\\n", - "0 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... NaN NaN \n", - "1 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "2 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "3 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "4 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... prefrontal func \n", + "0 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "1 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "2 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "3 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "4 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", "\n", - " fmap run scans session subject suffix task \n", - "0 NaN NaN NaN NaN 08 sessions NaN \n", - "1 NaN 2.0 NaN 2 08 bold rest \n", - "2 NaN 2.0 NaN 2 08 physio rest \n", - "3 NaN 1.0 NaN 2 08 bold rest \n", - "4 NaN NaN NaN 2 08 bold rest " + " fmap run scans session subject suffix task \n", + "0 magnitude1 1.0 NaN 2 08 magnitude1 NaN \n", + "1 NaN 2.0 NaN 2 08 phasediff NaN \n", + "2 phasediff 1.0 NaN 2 08 phasediff NaN \n", + "3 magnitude1 2.0 NaN 2 08 magnitude1 NaN \n", + "4 NaN 1.0 NaN 2 08 phasediff NaN " ] }, - "execution_count": 22, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -1079,7 +1119,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 17, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:26.693372Z", @@ -1125,81 +1165,81 @@ " \n", " \n", " \n", - " 1\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", + " 0\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", - " 2.0\n", + " fmap\n", + " magnitude1\n", + " 1.0\n", " NaN\n", " 2\n", " 08\n", - " bold\n", - " rest\n", + " magnitude1\n", + " NaN\n", " 6.0\n", " 4.0\n", " 35.0\n", " \n", " \n", - " 2\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", + " 1\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", + " NaN\n", + " fmap\n", " NaN\n", " 2.0\n", " NaN\n", " 2\n", " 08\n", - " physio\n", - " rest\n", + " phasediff\n", + " NaN\n", " 6.0\n", " 4.0\n", " 35.0\n", " \n", " \n", - " 3\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", + " 2\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", + " fmap\n", + " phasediff\n", " 1.0\n", " NaN\n", " 2\n", " 08\n", - " bold\n", - " rest\n", + " phasediff\n", + " NaN\n", " 6.0\n", " 4.0\n", " 35.0\n", " \n", " \n", - " 4\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " prefrontal\n", - " func\n", - " NaN\n", + " 3\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", + " fmap\n", + " magnitude1\n", + " 2.0\n", " NaN\n", " 2\n", " 08\n", - " bold\n", - " rest\n", + " magnitude1\n", + " NaN\n", " 6.0\n", " 4.0\n", " 35.0\n", " \n", " \n", - " 5\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " prefrontal\n", - " func\n", + " 4\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " NaN\n", + " fmap\n", " NaN\n", + " 1.0\n", " NaN\n", " 2\n", " 08\n", - " physio\n", - " rest\n", + " phasediff\n", + " NaN\n", " 6.0\n", " 4.0\n", " 35.0\n", @@ -1210,21 +1250,28 @@ ], "text/plain": [ " path acquisition datatype \\\n", - "1 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "2 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "3 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "4 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... prefrontal func \n", - "5 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... prefrontal func \n", + "0 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "1 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "2 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "3 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "4 /Users/tal/Dropbox/Code/pybids/bids/tests/data... NaN fmap \n", + "\n", + " fmap run scans session subject suffix task thirst vigilance \\\n", + "0 magnitude1 1.0 NaN 2 08 magnitude1 NaN 6.0 4.0 \n", + "1 NaN 2.0 NaN 2 08 phasediff NaN 6.0 4.0 \n", + "2 phasediff 1.0 NaN 2 08 phasediff NaN 6.0 4.0 \n", + "3 magnitude1 2.0 NaN 2 08 magnitude1 NaN 6.0 4.0 \n", + "4 NaN 1.0 NaN 2 08 phasediff NaN 6.0 4.0 \n", "\n", - " fmap run scans session subject suffix task thirst vigilance words \n", - "1 NaN 2.0 NaN 2 08 bold rest 6.0 4.0 35.0 \n", - "2 NaN 2.0 NaN 2 08 physio rest 6.0 4.0 35.0 \n", - "3 NaN 1.0 NaN 2 08 bold rest 6.0 4.0 35.0 \n", - "4 NaN NaN NaN 2 08 bold rest 6.0 4.0 35.0 \n", - "5 NaN NaN NaN 2 08 physio rest 6.0 4.0 35.0 " + " words \n", + "0 35.0 \n", + "1 35.0 \n", + "2 35.0 \n", + "3 35.0 \n", + "4 35.0 " ] }, - "execution_count": 23, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -1238,7 +1285,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 18, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:27.748194Z", @@ -1286,8 +1333,8 @@ " \n", " \n", " \n", - " 1\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", + " 9\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " fullbrain\n", " func\n", " NaN\n", @@ -1303,25 +1350,8 @@ " 60.0\n", " \n", " \n", - " 2\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " fullbrain\n", - " func\n", - " NaN\n", - " 2.0\n", - " NaN\n", - " 2\n", - " 08\n", - " physio\n", - " rest\n", - " bold\n", - " fullbrain\n", - " 75.0\n", - " 60.0\n", - " \n", - " \n", - " 3\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", + " 10\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " fullbrain\n", " func\n", " NaN\n", @@ -1329,7 +1359,7 @@ " NaN\n", " 2\n", " 08\n", - " bold\n", + " physio\n", " rest\n", " bold\n", " fullbrain\n", @@ -1337,8 +1367,8 @@ " 65.0\n", " \n", " \n", - " 4\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", + " 11\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", " prefrontal\n", " func\n", " NaN\n", @@ -1354,50 +1384,67 @@ " NaN\n", " \n", " \n", - " 5\n", - " /home/yoh/proj/bids/pybids/bids/tests/data/7t_...\n", - " prefrontal\n", + " 12\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", + " fullbrain\n", " func\n", " NaN\n", - " NaN\n", + " 2.0\n", " NaN\n", " 2\n", " 08\n", " physio\n", " rest\n", + " bold\n", + " fullbrain\n", + " 75.0\n", + " 60.0\n", + " \n", + " \n", + " 13\n", + " /Users/tal/Dropbox/Code/pybids/bids/tests/data...\n", + " fullbrain\n", + " func\n", " NaN\n", + " 1.0\n", " NaN\n", - " NaN\n", - " NaN\n", + " 2\n", + " 08\n", + " bold\n", + " rest\n", + " bold\n", + " fullbrain\n", + " 65.0\n", + " 65.0\n", " \n", " \n", "\n", "" ], "text/plain": [ - " path acquisition_x datatype \\\n", - "1 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "2 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "3 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... fullbrain func \n", - "4 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... prefrontal func \n", - "5 /home/yoh/proj/bids/pybids/bids/tests/data/7t_... prefrontal func \n", + " path acquisition_x datatype \\\n", + "9 /Users/tal/Dropbox/Code/pybids/bids/tests/data... fullbrain func \n", + "10 /Users/tal/Dropbox/Code/pybids/bids/tests/data... fullbrain func \n", + "11 /Users/tal/Dropbox/Code/pybids/bids/tests/data... prefrontal func \n", + "12 /Users/tal/Dropbox/Code/pybids/bids/tests/data... fullbrain func \n", + "13 /Users/tal/Dropbox/Code/pybids/bids/tests/data... fullbrain func \n", "\n", - " fmap run scans session subject suffix_x task suffix_y acquisition_y \\\n", - "1 NaN 2.0 NaN 2 08 bold rest bold fullbrain \n", - "2 NaN 2.0 NaN 2 08 physio rest bold fullbrain \n", - "3 NaN 1.0 NaN 2 08 bold rest bold fullbrain \n", - "4 NaN NaN NaN 2 08 bold rest NaN NaN \n", - "5 NaN NaN NaN 2 08 physio rest NaN NaN \n", + " fmap run scans session subject suffix_x task suffix_y acquisition_y \\\n", + "9 NaN 2.0 NaN 2 08 bold rest bold fullbrain \n", + "10 NaN 1.0 NaN 2 08 physio rest bold fullbrain \n", + "11 NaN NaN NaN 2 08 bold rest NaN NaN \n", + "12 NaN 2.0 NaN 2 08 physio rest bold fullbrain \n", + "13 NaN 1.0 NaN 2 08 bold rest bold fullbrain \n", "\n", - " future past \n", - "1 75.0 60.0 \n", - "2 75.0 60.0 \n", - "3 65.0 65.0 \n", - "4 NaN NaN \n", - "5 NaN NaN " + " future past \n", + "9 75.0 60.0 \n", + "10 65.0 65.0 \n", + "11 NaN NaN \n", + "12 75.0 60.0 \n", + "13 65.0 65.0 " ] }, - "execution_count": 24, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -1420,7 +1467,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 19, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:27.763448Z", @@ -1434,20 +1481,20 @@ "True" ] }, - "execution_count": 25, + "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Note that when using the bids validator, the filepath MUST be relative to the top level bids directory\n", - "validator = bids.layout.BIDSValidator()\n", + "validator = BIDSValidator()\n", "validator.is_bids('/sub-02/ses-01/anat/sub-02_ses-01_T2w.nii.gz')" ] }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 20, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:27.773052Z", @@ -1461,7 +1508,7 @@ "True" ] }, - "execution_count": 26, + "execution_count": 20, "metadata": {}, "output_type": "execute_result" } @@ -1473,7 +1520,7 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 21, "metadata": {}, "outputs": [ { @@ -1482,7 +1529,7 @@ "True" ] }, - "execution_count": 27, + "execution_count": 21, "metadata": {}, "output_type": "execute_result" } @@ -1494,7 +1541,7 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 22, "metadata": {}, "outputs": [ { @@ -1503,7 +1550,7 @@ "False" ] }, - "execution_count": 28, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } @@ -1515,7 +1562,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 23, "metadata": {}, "outputs": [ { @@ -1524,7 +1571,7 @@ "True" ] }, - "execution_count": 29, + "execution_count": 23, "metadata": {}, "output_type": "execute_result" } @@ -1535,7 +1582,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 24, "metadata": { "ExecuteTime": { "end_time": "2018-08-01T20:05:27.780022Z", @@ -1549,7 +1596,7 @@ "False" ] }, - "execution_count": 30, + "execution_count": 24, "metadata": {}, "output_type": "execute_result" } @@ -1569,9 +1616,9 @@ ], "metadata": { "kernelspec": { - "display_name": "pybids-venv3", + "display_name": "Python 3", "language": "python", - "name": "pybids-venv3" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -1583,7 +1630,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.5" + "version": "3.6.7" }, "toc": { "nav_menu": {},