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Update links to docs in some of the notebooks #186

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Update links to docs in some of the notebooks #186

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ebeb23f
Update link to docs in basic_data_input.ipynb
jankaWIS Mar 3, 2024
752ddf6
Update URL and some html tags in basic_data_output.ipynb
jankaWIS Mar 4, 2024
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2 changes: 1 addition & 1 deletion notebooks/basic_data_input.ipynb
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Expand Up @@ -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."
]
},
{
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20 changes: 10 additions & 10 deletions notebooks/basic_data_output.ipynb
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Expand Up @@ -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",
"<div class=\"alert alert-info\">\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 <a href=\"https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink\">DataSink</a>'s inputs are defined and created by using the workflow connect statement. Currently disconnecting an input from the <a href=\"https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#datasink\">DataSink</a> does not remove that connection port.\n",
"</div>\n",
"\n",
"Let's assume we have the following workflow.\n",
"\n",
"<img src=\"../static/images/datasink_flow.png\" width=\"160\">\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"
]
},
{
Expand Down Expand Up @@ -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."
]
},
{
Expand All @@ -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."
Expand All @@ -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."
]
},
{
Expand All @@ -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."
]
},
{
Expand All @@ -149,7 +149,7 @@
"\n",
"\n",
"<div class=\"alert alert-info\">\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",
" <b>Note:</b> 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",
"</div>"
]
},
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"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [default]",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -541,7 +541,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
"version": "3.6.10"
}
},
"nbformat": 4,
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