Skip to content

Folder

pynapple.io.folder

The Folder class helps to navigate a hierarchical data tree.

Folder

Bases: UserDict

Base class for all type of folders (i.e. Project, Subject, Sessions, ...). Handles files and sub-folders discovery

Attributes:

Name Type Description
data dict

Dictionary holidng all the pynapple objects found in the folder.
name str

Name of the folder
npz_files list

List of npz files found in the folder
nwb_files list

List of nwb files found in the folder
path str

Absolute path of the folder
subfolds dict

Dictionary of all the subfolders
Source code in pynapple/io/folder.py 
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
class Folder(UserDict):
    """
    Base class for all type of folders (i.e. Project, Subject, Sessions, ...).
    Handles files and sub-folders discovery

    Attributes
    ----------
    data : dict
        Dictionary holidng all the pynapple objects found in the folder.
    name : str
        Name of the folder
    npz_files : list
        List of npz files found in the folder
    nwb_files : list
        List of nwb files found in the folder
    path : str
        Absolute path of the folder
    subfolds : dict
        Dictionary of all the subfolders

    """

    def __init__(self, path):  # , exclude=(), max_depth=4):
        """Initialize the Folder object

        Parameters
        ----------
        path : str
            Path to the folder
        """
        path = Path(path)
        self.path = path
        self.name = self.path.name
        self._basic_view = Tree(
            ":open_file_folder: {}".format(self.name), guide_style="blue"
        )
        self._full_view = None

        # Search sub-folders
        subfolds = [
            p for p in path.iterdir() if p.is_dir() and not p.name.startswith(".")
        ]

        subfolds.sort()

        self.subfolds = {}

        for s in subfolds:
            sub = s.name
            self.subfolds[sub] = Folder(s)
            self._basic_view.add(":open_file_folder: [blue]" + sub)

        # Search files
        self.npz_files = _find_files(path, "npz")
        self.nwb_files = _find_files(path, "nwb")

        for filename, file in self.npz_files.items():
            self._basic_view.add("[green]" + file.name + " \t|\t " + file.type)

        for file in self.nwb_files.values():
            self._basic_view.add("[magenta]" + file.name + " \t|\t NWB file")

        # Putting everything together
        self.data = {**self.npz_files, **self.nwb_files, **self.subfolds}

        UserDict.__init__(self, self.data)

    def __str__(self):
        """View of the object"""
        with Console() as console:
            console.print(self._basic_view)
        return ""

    # def __repr__(self):
    #     """View of the object"""
    #     print(self._basic_view)

    def __getitem__(self, key):
        """Get subfolder or load file.

        Parameters
        ----------
        key : str

        Returns
        -------
        (Ts, Tsd, TsdFrame, TsGroup, IntervalSet, Folder or NWBFile)

        Raises
        ------
        KeyError
            If key is not in the dictionary
        """
        if key.__hash__:
            if self.__contains__(key):
                if isinstance(self.data[key], NPZFile):
                    data = self.data[key].load()
                    self.data[key] = data
                    # setattr(self, key, data)
                    return data
                elif isinstance(self.data[key], NWBFile):
                    return self.data[key]
                else:
                    return self.data[key]
            else:
                raise KeyError("Can't find key {} in group index.".format(key))

    # # # Gets called when an attribute is accessed
    # def __getattribute__(self, item):
    #     value = super(Folder, self).__getattribute__(item)

    #     if isinstance(value, NPZFile):
    #         data = value.load()
    #         setattr(self, item, data)
    #         self.data[item] = data
    #         return data
    #     else:
    #         return value

    def _generate_tree_view(self):
        tree = Tree(":open_file_folder: {}".format(self.name), guide_style="blue")

        # Folder
        for fold in self.subfolds.keys():
            tree.add(":open_file_folder: " + fold)
            _walk_folder(tree.children[-1], self.subfolds[fold])

        # NPZ files
        for file in self.npz_files.values():
            tree.add("[green]" + file.name + " \t|\t " + file.type)

        # NWB files
        for file in self.nwb_files.values():
            tree.add("[magenta]" + file.name + " \t|\t NWB file")

        self._full_view = tree

    def expand(self):
        """Display the full tree view. Equivalent to Folder.view"""
        if not isinstance(self._full_view, Tree):
            self._generate_tree_view()

        with Console() as console:
            console.print(self._full_view)

        return None

    @property
    def view(self):
        """Summary"""
        return self.expand()

    def save(self, name, obj, description=""):
        """Save a pynapple object in the folder in a single file in uncompressed ``.npz`` format.
        By default, the save function overwrite previously save file with the same name.

        Parameters
        ----------
        name : str
            Filename
        obj : Ts, Tsd, TsdFrame, TsGroup or IntervalSet
            Pynapple object.
        description : str, optional
            Metainformation added as a json sidecar.
        """
        filepath = self.path / (name + ".npz")
        obj.save(filepath)
        self.npz_files[name] = NPZFile(filepath)
        self.data[name] = obj

        metadata = {"time": str(datetime.now()), "info": str(description)}

        with open(self.path / (name + ".json"), "w") as ff:
            json.dump(metadata, ff, indent=2)

        # regenerate the tree view
        self._generate_tree_view()

    def load(self):
        """Load all compatible NPZ files."""
        for k in self.npz_files.keys():
            self[k] = self.npz_files[k].load()

    # def add_metadata(self):
    #     """Summary"""
    #     pass

    def info(self, name):
        """Display the metadata within the json sidecar of a NPZ file

        Parameters
        ----------
        name : str
            Name of the npz file
        """
        self.metadata(name)

    def doc(self, name):
        """Display the metadata within the json sidecar of a NPZ file

        Parameters
        ----------
        name : str
            Name of the npz file
        """
        self.metadata(name)

    def metadata(self, name):
        """Display the metadata within the json sidecar of a NPZ file

        Parameters
        ----------
        name : str
            Name of the npz file
        """
        # Search for json first
        json_filename = self.path / (name + ".json")
        title = self.path / (name + ".npz")
        if json_filename.exists():
            with open(json_filename, "r") as ff:
                metadata = json.load(ff)
                text = "\n".join([" : ".join(it) for it in metadata.items()])
            panel = Panel.fit(text, border_style="green", title=str(title))
        else:
            panel = Panel.fit(
                "No metadata",
                border_style="red",
                title=str(title),
            )
        with Console() as console:
            console.print(panel)

        return None

view property 

view

Summary

__init__ 

__init__(path)

Initialize the Folder object

Parameters:

Name Type Description Default
path str

Path to the folder

 required
Source code in pynapple/io/folder.py 
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
def __init__(self, path):  # , exclude=(), max_depth=4):
    """Initialize the Folder object

    Parameters
    ----------
    path : str
        Path to the folder
    """
    path = Path(path)
    self.path = path
    self.name = self.path.name
    self._basic_view = Tree(
        ":open_file_folder: {}".format(self.name), guide_style="blue"
    )
    self._full_view = None

    # Search sub-folders
    subfolds = [
        p for p in path.iterdir() if p.is_dir() and not p.name.startswith(".")
    ]

    subfolds.sort()

    self.subfolds = {}

    for s in subfolds:
        sub = s.name
        self.subfolds[sub] = Folder(s)
        self._basic_view.add(":open_file_folder: [blue]" + sub)

    # Search files
    self.npz_files = _find_files(path, "npz")
    self.nwb_files = _find_files(path, "nwb")

    for filename, file in self.npz_files.items():
        self._basic_view.add("[green]" + file.name + " \t|\t " + file.type)

    for file in self.nwb_files.values():
        self._basic_view.add("[magenta]" + file.name + " \t|\t NWB file")

    # Putting everything together
    self.data = {**self.npz_files, **self.nwb_files, **self.subfolds}

    UserDict.__init__(self, self.data)

__str__ 

__str__()

View of the object

Source code in pynapple/io/folder.py 
141
142
143
144
145
def __str__(self):
    """View of the object"""
    with Console() as console:
        console.print(self._basic_view)
    return ""

__getitem__ 

__getitem__(key)

Get subfolder or load file.

Parameters:

Name Type Description Default
key str
required

Returns:

Type Description
(Ts, Tsd, TsdFrame, TsGroup, IntervalSet, Folder or NWBFile)

Raises:

Type Description
KeyError

If key is not in the dictionary
Source code in pynapple/io/folder.py 
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
def __getitem__(self, key):
    """Get subfolder or load file.

    Parameters
    ----------
    key : str

    Returns
    -------
    (Ts, Tsd, TsdFrame, TsGroup, IntervalSet, Folder or NWBFile)

    Raises
    ------
    KeyError
        If key is not in the dictionary
    """
    if key.__hash__:
        if self.__contains__(key):
            if isinstance(self.data[key], NPZFile):
                data = self.data[key].load()
                self.data[key] = data
                # setattr(self, key, data)
                return data
            elif isinstance(self.data[key], NWBFile):
                return self.data[key]
            else:
                return self.data[key]
        else:
            raise KeyError("Can't find key {} in group index.".format(key))

expand 

expand()

Display the full tree view. Equivalent to Folder.view

Source code in pynapple/io/folder.py 
211
212
213
214
215
216
217
218
219
def expand(self):
    """Display the full tree view. Equivalent to Folder.view"""
    if not isinstance(self._full_view, Tree):
        self._generate_tree_view()

    with Console() as console:
        console.print(self._full_view)

    return None

save 

save(name, obj, description='')

Save a pynapple object in the folder in a single file in uncompressed .npz format. By default, the save function overwrite previously save file with the same name.

Parameters:

Name Type Description Default
name str

Filename

 required
obj (Ts, Tsd, TsdFrame, TsGroup or IntervalSet)

Pynapple object.

 required
description str

Metainformation added as a json sidecar.

 ''
Source code in pynapple/io/folder.py 
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
def save(self, name, obj, description=""):
    """Save a pynapple object in the folder in a single file in uncompressed ``.npz`` format.
    By default, the save function overwrite previously save file with the same name.

    Parameters
    ----------
    name : str
        Filename
    obj : Ts, Tsd, TsdFrame, TsGroup or IntervalSet
        Pynapple object.
    description : str, optional
        Metainformation added as a json sidecar.
    """
    filepath = self.path / (name + ".npz")
    obj.save(filepath)
    self.npz_files[name] = NPZFile(filepath)
    self.data[name] = obj

    metadata = {"time": str(datetime.now()), "info": str(description)}

    with open(self.path / (name + ".json"), "w") as ff:
        json.dump(metadata, ff, indent=2)

    # regenerate the tree view
    self._generate_tree_view()

load 

load()

Load all compatible NPZ files.

Source code in pynapple/io/folder.py 
252
253
254
255
def load(self):
    """Load all compatible NPZ files."""
    for k in self.npz_files.keys():
        self[k] = self.npz_files[k].load()

info 

info(name)

Display the metadata within the json sidecar of a NPZ file

Parameters:

Name Type Description Default
name str

Name of the npz file

 required
Source code in pynapple/io/folder.py 
261
262
263
264
265
266
267
268
269
def info(self, name):
    """Display the metadata within the json sidecar of a NPZ file

    Parameters
    ----------
    name : str
        Name of the npz file
    """
    self.metadata(name)

doc 

doc(name)

Display the metadata within the json sidecar of a NPZ file

Parameters:

Name Type Description Default
name str

Name of the npz file

 required
Source code in pynapple/io/folder.py 
271
272
273
274
275
276
277
278
279
def doc(self, name):
    """Display the metadata within the json sidecar of a NPZ file

    Parameters
    ----------
    name : str
        Name of the npz file
    """
    self.metadata(name)

metadata 

metadata(name)

Display the metadata within the json sidecar of a NPZ file

Parameters:

Name Type Description Default
name str

Name of the npz file

 required
Source code in pynapple/io/folder.py 
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
def metadata(self, name):
    """Display the metadata within the json sidecar of a NPZ file

    Parameters
    ----------
    name : str
        Name of the npz file
    """
    # Search for json first
    json_filename = self.path / (name + ".json")
    title = self.path / (name + ".npz")
    if json_filename.exists():
        with open(json_filename, "r") as ff:
            metadata = json.load(ff)
            text = "\n".join([" : ".join(it) for it in metadata.items()])
        panel = Panel.fit(text, border_style="green", title=str(title))
    else:
        panel = Panel.fit(
            "No metadata",
            border_style="red",
            title=str(title),
        )
    with Console() as console:
        console.print(panel)

    return None