Merge pull request #39 from skim0119/38_sample_data

Update: Sample dataset and utilities to install

fix 38

docs/examples/sample_datasets.rst

@@ -0,0 +1,20 @@
+Sample Datasets
+###############
+
+.. automodule:: miv.datasets
+
+.. warning::
+   The size of the datasets are typically very large. The download can take
+   a long time to complete.
+
+Raw Recording Samples
++++++++++++++++++++++
+
+.. automodule:: miv.datasets.optogenetic
+   :members:
+
+MiV Dataset Samples
++++++++++++++++++++
+
+.. automodule:: miv.datasets.criticality
+   :members:

docs/index.rst

@@ -52,7 +52,8 @@ If you are interested in contributing to this project, we prepared contribution
    :maxdepth: 2
    :caption: Example Scripts
 
-   examples/spike_detection
+   examples/sample_datasets
+.. examples/spike_detection
 
 .. toctree::
    :maxdepth: 2

miv/datasets/__init__.py

@@ -0,0 +1,9 @@
+__doc__ = """
+Sample datasets for debugging/testing.
+
+Any downloaded datasets will be saved in **datasets** directory.
+If the dataset already exists, download will be skipped.
+To remove any cache files, you can delete the **datasets** directory.
+"""
+
+from miv.datasets.optogenetic import load_data

miv/datasets/criticality.py

@@ -0,0 +1,40 @@
+__doc__ = """Sample data for criticality analysis."""
+__all__ = ["load_data"]
+
+import gzip
+import os
+
+import numpy as np
+
+from miv.datasets.utils import get_file
+
+
+def load_data():
+    """
+    Loads the sample for criticality analysis
+
+    Total size: 5.1 MB (compressed)
+
+    Returns
+    -------
+    datapath: str
+
+    Examples
+    --------
+        >>> from miv import datasets
+        >>> data = datasets.criticality.load_data()
+    """
+
+    subdir = "criticality"
+    base_url = "https://uofi.box.com/shared/static/mxj6mfjj0fdexod4nqoqovdeg7t8dbbq.mat"
+    file = "asdf.mat"
+    file_hash = "c8ff82f4700eed2023d37cb7643d24b37350e521469148406042ef206c3aac34"
+
+    path = get_file(
+        file_url=base_url,
+        cache_subdir=subdir,
+        fname=file,
+        file_hash=file_hash,
+        archive_format=None,
+    )
+    return path

miv/datasets/optogenetic.py

@@ -0,0 +1,80 @@
+__doc__ = """Sample signal readout from optogenetic neuron."""
+__all__ = ["load_data"]
+
+import gzip
+import os
+
+import numpy as np
+
+from miv.datasets.utils import get_file
+from miv.io import DataManager
+
+
+def load_data():
+    """
+    Loads the sample optogenetic experiment data.
+
+    Total size: 600.5 MB (compressed)
+
+    Notes
+    -----
+    All experiment are 1 minute long, 30k Hz recording of optogenetic
+    neuron cells over 64 channels MEA. Dataset includes 1 spontaneous
+    recording and 4 stimulated recording.
+
+    Spontaneous recording is the recording over 1 minute period without
+    external stimulation. The purpose was to measure the baseline mean-
+    firing rate.
+
+    Stimulation was done by LED light. Over 1 minute (60 seconds) period,
+    6 stimulation was done with 10 seconds of intervals. For each stimulation,
+    LED light was shined over 1 seconds, followed by remaining 9 seconds
+    of rest (without light).
+
+    Containing experiments:
+
+    * experiment0: spontaneous recording
+    * experiment1-4: stimulated recordings
+
+    Returns
+    -------
+    dataset: miv.io.DataManager
+
+    Examples
+    --------
+        >>> from miv import datasets
+        >>> experiments: miv.io.DataManager = datasets.opogenetic.load_data()
+        >>> experiments.tree()
+        2022-03-10_16-19-09
+            0: <miv.io.data.Data object at 0x7fbc30b9a9a0>
+               └── Record Node 104/experiment1/recording1
+            1: <miv.io.data.Data object at 0x7fbc2ae16700>
+               └── Record Node 104/experiment0/recording1
+            2: <miv.io.data.Data object at 0x7fbc2ac9e7c0>
+               └── Record Node 104/experiment2/recording2
+            3: <miv.io.data.Data object at 0x7fbc2ac9edc0>
+               └── Record Node 104/experiment3/recording1
+            4: <miv.io.data.Data object at 0x7fbc2ac9e160>
+               └── Record Node 104/experiment4/recording3
+
+    License
+    -------
+        ...
+
+    """
+
+    subdir = "optogenetic"
+    base_url = "https://uofi.box.com/shared/static/9llg11ods9iejdt2omjwjosbsxb5ui10.zip"
+    file = "2022-03-10_16-19-09.zip"
+    file_hash = "5deadc1b2a20501b5f6ee8828fa9c85df0b7890bd6ac4eaa8dca768d3b8b5f83"
+
+    path = get_file(
+        file_url=base_url,
+        cache_subdir=subdir,
+        fname=file,
+        file_hash=file_hash,
+        archive_format="zip",
+    )
+    experiment = DataManager(path)
+    experiment.tree()
+    return experiment