diff --git a/getting_started/03_file_management.ipynb b/getting_started/03_file_management.ipynb
index a677f0d0867b13e45ce59782acd44b90dc6d7447..b7a7cbd7ad4bc2f4d5ab151a4b21d4a183c86a6f 100644
--- a/getting_started/03_file_management.ipynb
+++ b/getting_started/03_file_management.ipynb
@@ -42,23 +42,24 @@
"\n",
"\n",
"* [Managing files and directories](#managing-files-and-directories)\n",
- " * [Querying and changing the current directory](#querying-and-changing-the-current-directory)\n",
- " * [Directory listings](#directory-listings)\n",
- " * [Creating and removing directories](#creating-and-removing-directories)\n",
- " * [Moving and removing files](#moving-and-removing-files)\n",
- " * [Walking a directory tree](#walking-a-directory-tree)\n",
- " * [Copying, moving, and removing directory trees](#copying-moving-and-removing-directory-trees)\n",
+ " * [Querying and changing the current directory](#querying-and-changing-the-current-directory)\n",
+ " * [Directory listings](#directory-listings)\n",
+ " * [Creating and removing directories](#creating-and-removing-directories)\n",
+ " * [Moving and removing files](#moving-and-removing-files)\n",
+ " * [Walking a directory tree](#walking-a-directory-tree)\n",
+ " * [Copying, moving, and removing directory trees](#copying-moving-and-removing-directory-trees)\n",
"* [Managing file paths](#managing-file-paths)\n",
- " * [File and directory tests](#file-and-directory-tests)\n",
- " * [Deconstructing paths](#deconstructing-paths)\n",
- " * [Absolute and relative paths](#absolute-and-relative-paths)\n",
- " * [Wildcard matching a.k.a. globbing](#wildcard-matching-aka-globbing)\n",
- " * [Expanding the home directory and environment variables](#expanding-the-home-directory-and-environment-variables)\n",
- " * [Cross-platform compatibility](#cross-platform-compatbility)\n",
+ " * [File and directory tests](#file-and-directory-tests)\n",
+ " * [Deconstructing paths](#deconstructing-paths)\n",
+ " * [Absolute and relative paths](#absolute-and-relative-paths)\n",
+ " * [Wildcard matching a.k.a. globbing](#wildcard-matching-aka-globbing)\n",
+ " * [Expanding the home directory and environment variables](#expanding-the-home-directory-and-environment-variables)\n",
+ " * [Cross-platform compatibility](#cross-platform-compatbility)\n",
+ "* [FileTrees](#filetree)\n",
"* [Exercises](#exercises)\n",
- " * [Re-name subject directories](#re-name-subject-directories)\n",
- " * [Re-organise a data set](#re-organise-a-data-set)\n",
- " * [Solutions](#solutions)\n",
+ " * [Re-name subject directories](#re-name-subject-directories)\n",
+ " * [Re-organise a data set](#re-organise-a-data-set)\n",
+ " * [Solutions](#solutions)\n",
"* [Appendix: Exceptions](#appendix-exceptions)\n",
"\n",
"\n",
@@ -79,7 +80,8 @@
"outputs": [],
"source": [
"import os\n",
- "import os.path as op"
+ "import os.path as op\n",
+ "from pathlib import Path"
]
},
{
@@ -111,13 +113,13 @@
"outputs": [],
"source": [
"cwd = os.getcwd()\n",
- "print('Current directory: {}'.format(cwd))\n",
+ "print(f'Current directory: {cwd}')\n",
"\n",
"os.chdir(op.expanduser('~'))\n",
- "print('Changed to: {}'.format(os.getcwd()))\n",
+ "print(f'Changed to: {os.get_cwd()}')\n",
"\n",
"os.chdir(cwd)\n",
- "print('Changed back to: {}'.format(cwd))"
+ "print(f'Changed back to: {cwd}')"
]
},
{
@@ -158,13 +160,13 @@
"source": [
"cwd = os.getcwd()\n",
"listing = os.listdir(cwd)\n",
- "print('Directory listing: {}'.format(cwd))\n",
+ "print(f'Directory listing: {cwd}')\n",
"print('\\n'.join(listing))\n",
"print()\n",
"\n",
"datadir = 'raw_mri_data'\n",
"listing = os.listdir(datadir)\n",
- "print('Directory listing: {}'.format(datadir))\n",
+ "print(f'Directory listing: {datadir}')\n",
"print('\\n'.join(listing))"
]
},
@@ -961,6 +963,40 @@
"cell_type": "markdown",
"metadata": {},
"source": [
+ "> The `Path` object in the built-in [`pathlib`](https://docs.python.org/3/library/pathlib.html) also has\n",
+ "> excellent cross-platform support. If you write your file management code using this class you are far less likely\n",
+ "> to get errors on Windows.\n",
+ "\n",
+ "<a class=\"anchor\" id=\"filetree\"></a>\n",
+ "## FileTree\n",
+ "`fslpy` also contains support for `FileTree` objects (docs are \n",
+ "[here](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.filetree.html)). \n",
+ "These `FileTree` objects provide a simple format to define a whole directory structure with multiple subjects, sessions,\n",
+ "scans, etc. In the `FileTree` format the dataset we have been looking at so far would be described by:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "tree_text = \"\"\"\n",
+ "raw_mri_data\n",
+ " subj_{subject}\n",
+ " rest.nii.gz\n",
+ " t1.nii\n",
+ " t2.nii\n",
+ " task.nii.gz\n",
+ "\"\"\""
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "FileTrees are discussed in more detail in the advanced `fslpy` practical.\n",
+ "\n",
"<a class=\"anchor\" id=\"exercises\"></a>\n",
"## Exercises\n",
"\n",
diff --git a/getting_started/03_file_management.md b/getting_started/03_file_management.md
index 0c4979a8a3321811f0381fdfb5277b63c75d999d..35ead5cbc6757a380ea8cf902fab94f7f35a4a9b 100644
--- a/getting_started/03_file_management.md
+++ b/getting_started/03_file_management.md
@@ -36,23 +36,24 @@ other sections as a reference. You might miss out on some neat tricks though.
* [Managing files and directories](#managing-files-and-directories)
- * [Querying and changing the current directory](#querying-and-changing-the-current-directory)
- * [Directory listings](#directory-listings)
- * [Creating and removing directories](#creating-and-removing-directories)
- * [Moving and removing files](#moving-and-removing-files)
- * [Walking a directory tree](#walking-a-directory-tree)
- * [Copying, moving, and removing directory trees](#copying-moving-and-removing-directory-trees)
+ * [Querying and changing the current directory](#querying-and-changing-the-current-directory)
+ * [Directory listings](#directory-listings)
+ * [Creating and removing directories](#creating-and-removing-directories)
+ * [Moving and removing files](#moving-and-removing-files)
+ * [Walking a directory tree](#walking-a-directory-tree)
+ * [Copying, moving, and removing directory trees](#copying-moving-and-removing-directory-trees)
* [Managing file paths](#managing-file-paths)
- * [File and directory tests](#file-and-directory-tests)
- * [Deconstructing paths](#deconstructing-paths)
- * [Absolute and relative paths](#absolute-and-relative-paths)
- * [Wildcard matching a.k.a. globbing](#wildcard-matching-aka-globbing)
- * [Expanding the home directory and environment variables](#expanding-the-home-directory-and-environment-variables)
- * [Cross-platform compatibility](#cross-platform-compatbility)
+ * [File and directory tests](#file-and-directory-tests)
+ * [Deconstructing paths](#deconstructing-paths)
+ * [Absolute and relative paths](#absolute-and-relative-paths)
+ * [Wildcard matching a.k.a. globbing](#wildcard-matching-aka-globbing)
+ * [Expanding the home directory and environment variables](#expanding-the-home-directory-and-environment-variables)
+ * [Cross-platform compatibility](#cross-platform-compatbility)
+* [FileTrees](#filetree)
* [Exercises](#exercises)
- * [Re-name subject directories](#re-name-subject-directories)
- * [Re-organise a data set](#re-organise-a-data-set)
- * [Solutions](#solutions)
+ * [Re-name subject directories](#re-name-subject-directories)
+ * [Re-organise a data set](#re-organise-a-data-set)
+ * [Solutions](#solutions)
* [Appendix: Exceptions](#appendix-exceptions)
@@ -69,6 +70,7 @@ creating, removing, and traversing directories.
```
import os
import os.path as op
+from pathlib import Path
```
@@ -92,13 +94,13 @@ You can query and change the current directory with the `os.getcwd` and
```
cwd = os.getcwd()
-print('Current directory: {}'.format(cwd))
+print(f'Current directory: {cwd}')
os.chdir(op.expanduser('~'))
-print('Changed to: {}'.format(os.getcwd()))
+print(f'Changed to: {os.get_cwd()}')
os.chdir(cwd)
-print('Changed back to: {}'.format(cwd))
+print(f'Changed back to: {cwd}')
```
@@ -123,13 +125,13 @@ command):
```
cwd = os.getcwd()
listing = os.listdir(cwd)
-print('Directory listing: {}'.format(cwd))
+print(f'Directory listing: {cwd}')
print('\n'.join(listing))
print()
datadir = 'raw_mri_data'
listing = os.listdir(datadir)
-print('Directory listing: {}'.format(datadir))
+print(f'Directory listing: {datadir}')
print('\n'.join(listing))
```
@@ -730,6 +732,27 @@ print(path)
print(op.join(op.sep, 'home', 'fsluser', '.bash_profile'))
```
+> The `Path` object in the built-in [`pathlib`](https://docs.python.org/3/library/pathlib.html) also has
+> excellent cross-platform support. If you write your file management code using this class you are far less likely
+> to get errors on Windows.
+
+<a class="anchor" id="filetree"></a>
+## FileTree
+`fslpy` also contains support for `FileTree` objects (docs are
+[here](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.filetree.html)).
+These `FileTree` objects provide a simple format to define a whole directory structure with multiple subjects, sessions,
+scans, etc. In the `FileTree` format the dataset we have been looking at so far would be described by:
+```
+tree_text = """
+raw_mri_data
+ subj_{subject}
+ rest.nii.gz
+ t1.nii
+ t2.nii
+ task.nii.gz
+"""
+```
+FileTrees are discussed in more detail in the advanced `fslpy` practical.
<a class="anchor" id="exercises"></a>
## Exercises