diff --git a/notebooks/basic_data_input.ipynb b/notebooks/basic_data_input.ipynb index 2857f8c..de87cb3 100644 --- a/notebooks/basic_data_input.ipynb +++ b/notebooks/basic_data_input.ipynb @@ -17,7 +17,7 @@ " SelectFiles\n", " XNATSource\n", "\n", - "This tutorial will only cover some of them. For the rest, see the section [``interfaces.io``](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html) on the official homepage." + "This tutorial will only cover some of them. For the rest, see the section [``interfaces.io``](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html) on the official homepage." ] }, { diff --git a/notebooks/basic_data_output.ipynb b/notebooks/basic_data_output.ipynb index 959cccc..e7f872f 100644 --- a/notebooks/basic_data_output.ipynb +++ b/notebooks/basic_data_output.ipynb @@ -23,17 +23,17 @@ "source": [ "# DataSink\n", "\n", - "A workflow working directory is like a **cache**. It contains not only the outputs of various processing stages, it also contains various extraneous information such as execution reports, hashfiles determining the input state of processes. All of this is embedded in a hierarchical structure that reflects the iterables that have been used in the workflow. This makes navigating the working directory a not so pleasant experience. And typically the user is interested in preserving only a small percentage of these outputs. The [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) interface can be used to extract components from this `cache` and store it at a different location. For XNAT-based storage, see [XNATSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#nipype-interfaces-io-xnatsink).\n", + "A workflow working directory is like a **cache**. It contains not only the outputs of various processing stages, it also contains various extraneous information such as execution reports, hashfiles determining the input state of processes. All of this is embedded in a hierarchical structure that reflects the iterables that have been used in the workflow. This makes navigating the working directory a not so pleasant experience. And typically the user is interested in preserving only a small percentage of these outputs. The [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) interface can be used to extract components from this `cache` and store it at a different location. For XNAT-based storage, see [XNATSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#xnatsink).\n", "\n", "
\n", - "Unlike other interfaces, a [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink)'s inputs are defined and created by using the workflow connect statement. Currently disconnecting an input from the [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) does not remove that connection port.\n", + "Unlike other interfaces, a DataSink's inputs are defined and created by using the workflow connect statement. Currently disconnecting an input from the DataSink does not remove that connection port.\n", "
\n", "\n", "Let's assume we have the following workflow.\n", "\n", "\n", "\n", - "The following code segment defines the [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) node and sets the `base_directory` in which all outputs will be stored. The `container` input creates a subdirectory within the `base_directory`. If you are iterating a workflow over subjects, it may be useful to save it within a folder with the subject id.\n" + "The following code segment defines the [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) node and sets the `base_directory` in which all outputs will be stored. The `container` input creates a subdirectory within the `base_directory`. If you are iterating a workflow over subjects, it may be useful to save it within a folder with the subject id.\n" ] }, { @@ -85,7 +85,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The period (.) indicates that a subfolder called par should be created. But if we wanted to store it in the same folder as the realigned files, we would use the `.@` syntax. The @ tells the [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) interface to not create the subfolder. This will allow us to create different named input ports for [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) and allow the user to store the files in the same folder." + "The period (.) indicates that a subfolder called par should be created. But if we wanted to store it in the same folder as the realigned files, we would use the `.@` syntax. The @ tells the [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) interface to not create the subfolder. This will allow us to create different named input ports for [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) and allow the user to store the files in the same folder." ] }, { @@ -102,7 +102,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The syntax for the input port of [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) takes the following form:\n", + "The syntax for the input port of [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) takes the following form:\n", "\n", " string[[.[@]]string[[.[@]]string] ...]\n", " where parts between paired [] are optional." @@ -114,7 +114,7 @@ "source": [ "## MapNode\n", "\n", - "In order to use [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) inside a MapNode, its inputs have to be defined inside the constructor using the `infields` keyword arg." + "In order to use [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) inside a MapNode, its inputs have to be defined inside the constructor using the `infields` keyword arg." ] }, { @@ -123,7 +123,7 @@ "source": [ "## Parameterization\n", "\n", - "As discussed in [Iterables](basic_iteration.ipynb), one can run a workflow iterating over various inputs using the iterables attribute of nodes. This means that a given workflow can have multiple outputs depending on how many iterables are there. Iterables create working directory subfolders such as `_iterable_name_value`. The `parameterization` input parameter controls whether the data stored using [DataSink](http://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.io.html#datasink) is in a folder structure that contains this iterable information or not. It is generally recommended to set this to `True` when using multiple nested iterables." + "As discussed in [Iterables](basic_iteration.ipynb), one can run a workflow iterating over various inputs using the iterables attribute of nodes. This means that a given workflow can have multiple outputs depending on how many iterables are there. Iterables create working directory subfolders such as `_iterable_name_value`. The `parameterization` input parameter controls whether the data stored using [DataSink](https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink) is in a folder structure that contains this iterable information or not. It is generally recommended to set this to `True` when using multiple nested iterables." ] }, { @@ -149,7 +149,7 @@ "\n", "\n", "
\n", - "**Note**: In order to figure out which substitutions are needed it is often useful to run the workflow on a limited set of iterables and then determine the substitutions.\n", + " Note: In order to figure out which substitutions are needed it is often useful to run the workflow on a limited set of iterables and then determine the substitutions.\n", "
" ] }, @@ -527,7 +527,7 @@ "metadata": { "anaconda-cloud": {}, "kernelspec": { - "display_name": "Python [default]", + "display_name": "Python 3", "language": "python", "name": "python3" }, @@ -541,7 +541,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.5" + "version": "3.6.10" } }, "nbformat": 4,