nex5file

Name	nex5file JSON
Version	0.1.3 JSON
	download
home_page
Summary	Read and write .nex and .nex5 files and edit data stored in .nex and .nex5 files.
upload_time	2023-10-07 17:30:04
maintainer
docs_url	None
author
requires_python	>=3.7
license
keywords	neuroexplorer nex nex5 .nex .nex5
VCS
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requirements	No requirements were recorded.
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            # nex5file
Python package to read, write and edit data stored in NeuroExplorer .nex and .nex5 files

## Getting Started

### Install nex5file package

Run this command in Windows Command Prompt:
```
pip install -U nex5file
```

### Read .nex and .nex5 Files

`ReadNexFile` method of `nex5file.reader.Reader` class reads and parses contents of a .nex or a .nex5 file and returns an instance of `nex5file.filedata.FileData` object. This method reads all the data in the file.

```python
from nex5file.reader import Reader
from nex5file.filedata import FileData
nexFilePath = r"C:\path\to\your\file.nex"
reader = Reader()
data = reader.ReadNexFile(nexFilePath)
```

If you need to read only some channels from a .nex or .nex5 file, use `ReadNexFileVariables` method:

```python
# read only two continuous channels: cont1 and cont2
from nex5file.reader import Reader
from nex5file.filedata import FileData
nexFilePath = r"C:\path\to\your\file.nex"
reader = Reader()
data = reader.ReadNexFileVariables(nexFilePath, ['cont1', 'cont2'])
```

To retrieve channel names from a file, use `ReadNexHeadersOnly` method. Here is the code to read only continuous channels:

```python
# read only all continuous channels
from nex5file.reader import Reader
from nex5file.filedata import FileData
reader = Reader()
data = reader.ReadNexHeadersOnly(r"C:\path\to\your\file.nex")
contNames = data.ContinuousNames()
data_cont = reader.ReadNexFileVariables(r"C:\path\to\your\file.nex", contNames)
```

### Access Data in a FileData Object

Retrieving information fromm `FileData` object is similar to retrieving values using `nex` package. The difference is that `nex` package requires `NeuroExplorer` to be installed and running, while `nex5file` package if pure Python.

The syntax for accessing data is similar to `nex` package syntax. Many method names in `nex5file` package are the same as in `nex` package.

Here is a script to get continuous channels information using `nex`:

```python
import nex
doc = nex.OpenDocument(nexFilePath)
# print continuous channel name, sampling rates and continuous values
for name in doc.ContinuousNames():
    rate = doc[name].SamplingRate()
    values = doc[name].ContinuousValues()
    print(name, rate, values)
```

Here is the same functionality using `nex5file` package:

```python
from nex5file.reader import Reader
from nex5file.filedata import FileData

reader = Reader()
data = reader.ReadNexFile(nexFilePath)
# print continuous channel names, sampling rates and continuous values
for name in data.ContinuousNames():
    rate = data[name].SamplingRate()
    values = doc[name].ContinuousValues()
    print(name, rate, values)
```

### Modify Data in a FileData Object

You can use the following `FileData` methods to modify data:

- `DeleteVariable`
- `AddEvent`
- `AddNeuron`
- `AddIntervalAsPairsStartEnd`
- `AddMarker`
- `AddContVarWithFloatsSingleFragment`
- `AddContSingleFragmentValuesInt16`
- `AddContVarWithFloatsAllTimestamps`
- `AddWaveVarWithFloats`

### Write .nex and .nex5 Files

Use `WriteNexFile` method of `nex5file.writer.Writer` class

```python
from nex5file.writer import Writer
from nex5file.filedata import FileData
import numpy as np

freq = 100000
data = FileData(freq)

eName = "event 001"
eventTs = [1, 2, 3.5]
data.AddEvent(eName, np.array(eventTs))

nName = "neuron 002"
neuronTs = [0.001, 2.54, 8.99]
data.AddNeuron(nName, np.array(neuronTs))

nexFilePath = r"C:\path\to\your\file.nex"
writer = Writer()
writer.WriteNexFile(data, nexFilePath)
```

See [www.neuroexplorer.com/nex5file/](https://www.neuroexplorer.com/nex5file/) for nex5file reference documentation.

            

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    "description": "# nex5file\r\nPython package to read, write and edit data stored in NeuroExplorer .nex and .nex5 files\r\n\r\n## Getting Started\r\n\r\n### Install nex5file package\r\n\r\nRun this command in Windows Command Prompt:\r\n```\r\npip install -U nex5file\r\n```\r\n\r\n### Read .nex and .nex5 Files\r\n\r\n`ReadNexFile` method of `nex5file.reader.Reader` class reads and parses contents of a .nex or a .nex5 file and returns an instance of `nex5file.filedata.FileData` object. This method reads all the data in the file.\r\n\r\n```python\r\nfrom nex5file.reader import Reader\r\nfrom nex5file.filedata import FileData\r\nnexFilePath = r\"C:\\path\\to\\your\\file.nex\"\r\nreader = Reader()\r\ndata = reader.ReadNexFile(nexFilePath)\r\n```\r\n\r\nIf you need to read only some channels from a .nex or .nex5 file, use `ReadNexFileVariables` method:\r\n\r\n```python\r\n# read only two continuous channels: cont1 and cont2\r\nfrom nex5file.reader import Reader\r\nfrom nex5file.filedata import FileData\r\nnexFilePath = r\"C:\\path\\to\\your\\file.nex\"\r\nreader = Reader()\r\ndata = reader.ReadNexFileVariables(nexFilePath, ['cont1', 'cont2'])\r\n```\r\n\r\nTo retrieve channel names from a file, use `ReadNexHeadersOnly` method. Here is the code to read only continuous channels:\r\n\r\n```python\r\n# read only all continuous channels\r\nfrom nex5file.reader import Reader\r\nfrom nex5file.filedata import FileData\r\nreader = Reader()\r\ndata = reader.ReadNexHeadersOnly(r\"C:\\path\\to\\your\\file.nex\")\r\ncontNames = data.ContinuousNames()\r\ndata_cont = reader.ReadNexFileVariables(r\"C:\\path\\to\\your\\file.nex\", contNames)\r\n```\r\n\r\n### Access Data in a FileData Object\r\n\r\nRetrieving information fromm `FileData` object is similar to retrieving values using `nex` package. The difference is that `nex` package requires `NeuroExplorer` to be installed and running, while `nex5file` package if pure Python.\r\n\r\nThe syntax for accessing data is similar to `nex` package syntax. Many method names in `nex5file` package are the same as in `nex` package.\r\n\r\nHere is a script to get continuous channels information using `nex`:\r\n\r\n```python\r\nimport nex\r\ndoc = nex.OpenDocument(nexFilePath)\r\n# print continuous channel name, sampling rates and continuous values\r\nfor name in doc.ContinuousNames():\r\n    rate = doc[name].SamplingRate()\r\n    values = doc[name].ContinuousValues()\r\n    print(name, rate, values)\r\n```\r\n\r\nHere is the same functionality using `nex5file` package:\r\n\r\n```python\r\nfrom nex5file.reader import Reader\r\nfrom nex5file.filedata import FileData\r\n\r\nreader = Reader()\r\ndata = reader.ReadNexFile(nexFilePath)\r\n# print continuous channel names, sampling rates and continuous values\r\nfor name in data.ContinuousNames():\r\n    rate = data[name].SamplingRate()\r\n    values = doc[name].ContinuousValues()\r\n    print(name, rate, values)\r\n```\r\n\r\n### Modify Data in a FileData Object\r\n\r\nYou can use the following `FileData` methods to modify data:\r\n\r\n- `DeleteVariable`\r\n- `AddEvent`\r\n- `AddNeuron`\r\n- `AddIntervalAsPairsStartEnd`\r\n- `AddMarker`\r\n- `AddContVarWithFloatsSingleFragment`\r\n- `AddContSingleFragmentValuesInt16`\r\n- `AddContVarWithFloatsAllTimestamps`\r\n- `AddWaveVarWithFloats`\r\n\r\n### Write .nex and .nex5 Files\r\n\r\nUse `WriteNexFile` method of `nex5file.writer.Writer` class\r\n\r\n```python\r\nfrom nex5file.writer import Writer\r\nfrom nex5file.filedata import FileData\r\nimport numpy as np\r\n\r\nfreq = 100000\r\ndata = FileData(freq)\r\n\r\neName = \"event 001\"\r\neventTs = [1, 2, 3.5]\r\ndata.AddEvent(eName, np.array(eventTs))\r\n\r\nnName = \"neuron 002\"\r\nneuronTs = [0.001, 2.54, 8.99]\r\ndata.AddNeuron(nName, np.array(neuronTs))\r\n\r\nnexFilePath = r\"C:\\path\\to\\your\\file.nex\"\r\nwriter = Writer()\r\nwriter.WriteNexFile(data, nexFilePath)\r\n```\r\n\r\nSee [www.neuroexplorer.com/nex5file/](https://www.neuroexplorer.com/nex5file/) for nex5file reference documentation.\r\n",
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