hansel 0.9.6

Quick Intro

Imagine this folder tree:

data
└── raw
    ├── 0040000
    │   └── session_1
    │       ├── anat_1
    │       └── rest_1
    ├── 0040001
    │   └── session_1
    │       ├── anat_1
    │       └── rest_1
    ├── 0040002
    │   └── session_1
    │       ├── anat_1
    │       └── rest_1
    ├── 0040003
    │   └── session_1
    │       ├── anat_1
    │       └── rest_1
    ├── 0040004
    │   └── session_1
    │       ├── anat_1
    │       └── rest_1

>>> from hansel import Crumb

# create the crumb
>>> crumb = Crumb("{base_dir}/data/raw/{subject_id}/{session_id}/{image_type}/{image}")

# set the base_dir path
>>> crumb = crumb.replace(base_dir='/home/hansel')
>>> print(str(crumb))
/home/hansel/data/raw/{subject_id}/{session_id}/{image_type}

# get the ids of the subjects
>>> subj_ids = crumb['subject_id']
>>> print(subj_ids)
['0040000', '0040001', '0040002', '0040003', '0040004', '0040005', ...

# get the paths to the subject folders, the output can be strings or crumbs,
# you choose with the ``make_crumbs`` boolean argument. Default: True.
>>> subj_paths = crumb.ls('subject_id', make_crumbs=True)
>>> print(subj_paths)
[Crumb("/home/hansel/data/raw/0040000/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040001/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040002/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040003/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040004/{session_id}/{image_type}/{image}"),
 ...

# set the image_type
>>> anat_crumb = crumb.replace(image_type='anat_1')
>>> print(anat_crumb)
/home/hansel/data/raw/{subject_id}/{session_id}/anat_1/{image}

# get the paths to the images inside the anat_1 folders
>>> anat_paths = anat_crumb.ls('image')
>>> print(anat_paths)
[Crumb("/home/hansel/data/raw/0040000/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040001/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040002/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040003/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040004/session_1/anat_1/mprage.nii.gz"),
 ...

# get the ``session_id`` of each of these ``anat_paths``
>>> sessions = [cr['session_id'][0] for cr in anat_paths]
>>> print(sessions)
['session_1', 'session_1', 'session_1', 'session_1', 'session_1', ...

# if you don't want the the output to be ``Crumbs`` but string paths:
>>> anat_paths = anat_crumb.ls('image', make_crumbs=False)
>>> print(anat_paths)
["/home/hansel/data/raw/0040000/session_1/anat_1/mprage.nii.gz",
 "/home/hansel/data/raw/0040001/session_1/anat_1/mprage.nii.gz",
 "/home/hansel/data/raw/0040002/session_1/anat_1/mprage.nii.gz",
 "/home/hansel/data/raw/0040003/session_1/anat_1/mprage.nii.gz",
 "/home/hansel/data/raw/0040004/session_1/anat_1/mprage.nii.gz",
 ...

# you can also use a list of ``fnmatch`` expressions to ignore certain files patterns
# using the ``ignore_list`` argument in the constructor.
# For example, the files that start with '.'.
>>> crumb = Crumb("{base_dir}/data/raw/{subject_id}/{session_id}/{image_type}/{image}",
>>>               ignore_list=['.*'])

Once you have a fully defined Crumb, you can use its path for operations with the corresponding file. For that you have to convert it to string by using str(crumb) or crumb.path.

See more quick examples after the Long Intro check More features and tricks.

Long Intro

I often find myself in a work related with structured folder paths, such as the one shown above.

I have tried many ways of solving these situations: loops, dictionaries, configuration files, etc. I always end up doing a different thing for the same problem over and over again.

This week I grew tired of it and decided to make a representation of a structured folder tree in a string and access it the most easy way.

If you look at the folder structure above I have:

• the root directory from where it is hanging: ...data/raw,

• many identifiers (in this case a subject identification), e.g., 0040000,

• session identification, session_1 and

• a data type (in this case an image type), anat_1 and rest_1.

With hansel I can represent this folder structure like this:

>>> from hansel import Crumb
>>> crumb = Crumb("{base_dir}/data/raw/{subject_id}/{session_id}/{image_type}/{image}")

Let’s say we have the structure above hanging from a base directory like /home/hansel/.

I can use the replace function to make set the base_dir parameter:

>>> crumb = crumb.replace(base_dir='/home/hansel')
>>> print(str(crumb))
/home/hansel/data/raw/{subject_id}/{session_id}/{image_type}

if I don’t need a copy of crumb, I can use the [] operator:

>>> crumb['base_dir'] = '/home/hansel'
>>> print(str(crumb))
/home/hansel/data/raw/{subject_id}/{session_id}/{image_type}

Now that the root path of my dataset is set, I can start querying my crumb path.

If I want to know the path to the existing subject_id folders:

We can use the ls function. Its output can be str or Crumb. I can choose this using the make_crumbs argument (default: True):

>>> subj_crumbs = crumb.ls('subject_id')
>>> print(subj_crumbs)
[Crumb("/home/hansel/data/raw/0040000/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040001/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040002/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040003/{session_id}/{image_type}/{image}"),
 Crumb("/home/hansel/data/raw/0040004/{session_id}/{image_type}/{image}"),
 ...

>>> subj_paths = anat_crumb.ls('subject_id', make_crumbs=False)
>>> print(subj_paths)
["/home/hansel/data/raw/0040000/{session_id}/{image_type}/{image}",
 "/home/hansel/data/raw/0040001/{session_id}/{image_type}/{image}",
 "/home/hansel/data/raw/0040002/{session_id}/{image_type}/{image}",
 "/home/hansel/data/raw/0040003/{session_id}/{image_type}/{image}",
 "/home/hansel/data/raw/0040004/{session_id}/{image_type}/{image}",
 ...

If I want to know what are the existing subject_id:

>>> subj_ids = crumb.ls('subject_id', fullpath=False)
>>> print(subj_ids)
['0040000', '0040001', '0040002', '0040003', '0040004', '0040005', ...

or

>>> subj_ids = crumb['subject_id']
>>> print(subj_ids)
['0040000', '0040001', '0040002', '0040003', '0040004', '0040005', ...

Now, if I wanted to get the path to all the images inside the anat_1 folders, I could do this:

>>> anat_crumb = crumb.replace(image_type='anat_1')
>>> print(anat_crumb)
/home/hansel/data/raw/{subject_id}/{session_id}/anat_1/{image}

or if I don’t need to keep a copy of crumb:

>>> crumb['image_type'] = 'anat_1'

# get the paths to the images inside the anat_1 folders
>>> anat_paths = crumb.ls('image')
>>> print(anat_paths)
[Crumb("/home/hansel/data/raw/0040000/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040001/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040002/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040003/session_1/anat_1/mprage.nii.gz"),
 Crumb("/home/hansel/data/raw/0040004/session_1/anat_1/mprage.nii.gz"),
 ...

Remember that I can still access the replaced crumb arguments in each of the previous crumbs in anat_paths.

>>> subj_ids = [cr['subject_id'][0] for cr in anat_paths]
>>> print(subj_ids)
['0040000', '0040001', '0040002', '0040003', '0040004', '0040005', ...

>>> files = [cr['image'][0] for cr in anat_paths]
>>> print(files)
['mprage.nii.gz', 'mprage.nii.gz', 'mprage.nii.gz', 'mprage.nii.gz', ...

More features and tricks

There are more possibilities such as:

Code

Github

You can check the latest sources with the command:

git clone https://www.github.com/alexsavio/hansel.git

or if you have write privileges:

git clone git@github.com:alexsavio/hansel.git

If you are going to create patches for this project, create a branch for it from the master branch.

We tag stable releases in the repository with the version number.

Testing

We are using py.test to help us with the testing.

Otherwise you can run the tests executing:

python setup.py test

or

py.test

or

make test

Version 0.9.0 - 0.9.6

• “cli diff” and “cli intersect” have the same interface.

• changed how “cli intersect” prints results. Added ‘base_crumb’ option.

• added to CLI default ignore list for crumbs: [‘.*’].

• add crumb diff to CLI.

• add difference utility function with test.

• add test__utils.py as a WIP.

• move CLI to click.

• Annoying bug fixed.

• Add crumb_copy.

• Now it doesn’t bother with relative paths.

• Fix crumb_copy for existing paths and linking relative paths.

• Add crumb_copy CLI.

• Make click a dependency and move crumb_copy to crumb copy.

• Add crumb ls and crumb intersect CLI.

• Add is_crumb_arg function to utils.

• Fix error in crumb copy parameter names.

Version 0.8.0 - 0.8.3

• Set to True the default value for check_exists in Crumb.ls function. I don’t think anybody is interested in non-existing paths.

• Now it is possible to set a non-open item in a Crumb, i.e., I can replace the value for an already set crumb argument.

• Update README.rst

• Code clean-up.

• Replace dict to OrderedDict output in valuesmap_to_dict function.

• Add regex option within arg_name argument of ls and __get_item__.

Version 0.7.0 - 0.7.5

• Refactoring of how Crumb works, now using string.Formatter. This will help with new features due to simpler logic.Now it is not possible to change the syntax of the Crumbs, although I guess nobody is interested in that.

• Fixed a few bugs from previous versions.

• Now copy function is not a classmethod anymore, so you can do crumb.copy() as well as Crumb.copy(crumb).

• patterns is not a dictionary anymore, the regexes are embedded in the _path string. The property patterns returns the dictionary as before. The function set_pattern must be used instead to set a different pattern to a given argument.

• Update README.rst

• Fix README.rst because of bad syntax for PyPI.

• Fix bug for Python 2.7

• Fix the bug in .rst for PyPI.

• Code cleanup

Version 0.6.0 - 0.6.2

• Added intersection function in utils.py.

• Change of behaviour in __getitem__, now it returns a list of values even if is only the one replace string from _argval.

• General renaming of the private functions inside Crumbs, more in accordance to the open_args/all_args idea.

• Fixed a few bugs and now the generated crumbs from unfold and ls will have the same parameters as the original Crumb.

• Change the behaviour or intersection with len(arg_names) == 1 for compatibility with crumb.build_path function.

• Improve README, update with new examples using intersection.

• Add pandas helper functions.

• Add utils to convert from values_maps to dicts.

• Improve docstrings.

Version 0.5.0 - 0.5.5

• Add Python 2.7 compatibility. Friends don’t let friends use Python 2.7!

• Add ‘re.ignorecase’ option for the regex argument in the constructor.

• Add utils.check_path function.

• Fix Crumb.split function to return the not defined part of the crumb.

• Add Crumbs.keys() function.

• Rename utils.remove_duplicates() to utils.rm_dups().

• Deprecating Crumbs.keys() function.

• Renamed Crumbs.keys() to Crumbs.open_args() and added Crumbs.all_args().

• Substitute the internal logic of Crumbs to work with Crumbs.open_args(), made it a bit faster.

• Added CHANGES.rst to MANIFEST.in

Version 0.4.0 - 0.4.2

• Fill CHANGES.rst.

• All outputs from Crumb.ls function will be sorted.

• Add regular expressions or fnmatch option for crumb arguments.

• Change exists behaviour. Now the empty crumb arguments will return False when exist().

• Code clean up.

• Fix bugs.

• Fix CHANGES.rst to correct restview in PyPI.

• Thanks to restview: https://pypi-hypernode.com/pypi/restview. Use: restview --long-description

• Improve documentation in README.

• Rename member _argreg to patterns, so the user can use it to manage the argument patterns.

Version 0.3.0 - 0.3.1

• Add _argval member, a dict which stores crumb arguments replacements.

• Add tests.

• Remove rm_dups option in Crumb.ls function.

• Remove conversion to Paths when Crumb has no crumb arguments in Crumb.ls.

• Fix README.

• Code clean up.

Version 0.2.0

• Add ignore_list parameter in Crumb constructor.

Version 0.1.0 - 0.1.1

• Simplify code.

• Increase test coverage.

• Add exist_check to Crumb.ls function.

• Fix bugs.

• Add Crumb.unfold function.

• Move mktree out of Crumb class.