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bmtool-0.2.3
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BMTools
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | bmtool-0.2.3 |
| نام | bmtool |
| نسخه کتابخانه | 0.2.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Tyler Banks |
| ایمیل نویسنده | tbanks@mail.missouri.edu |
| آدرس صفحه اصلی | https://github.com/tjbanks/bmtools |
| آدرس اینترنتی | https://pypi.org/project/bmtool/ |
| مجوز | MIT |
# bmtools
A collection of scripts to make developing networks in BMTK easier.
[](https://github.com/tjbanks/bmtool/blob/master/LICENSE)
## Getting Started
**Installation**
```bash
pip install bmtool
```
For developers who will be pulling down additional updates to this repository regularly use the following instead.
```bash
git clone https://github.com/tjbanks/bmtools
cd bmtools
python setup.py develop
```
Then download updates (from this directory) with
```
git pull
```
**Example Use**
```bash
> cd your_bmtk_model_directory
> bmtools
Usage: bmtools [OPTIONS] COMMAND [ARGS]...
Options:
--verbose Verbose printing
--help Show this message and exit.
Commands:
debug
plot
util
>
> bmtools plot
Usage: bmtools plot [OPTIONS] COMMAND [ARGS]...
Options:
--config PATH Configuration file to use, default: "simulation_config.json"
--no-display When set there will be no plot displayed, useful for saving
plots
--help Show this message and exit.
Commands:
connection Display information related to neuron connections
positions Plot cell positions for a given set of populations
raster Plot the spike raster for a given population
report Plot the specified report using BMTK's default report plotter
>
> bmtools plot positions
```
## Plotting Configuration
BMTools utilizes the default `simulation-config.json` file to know which data files built by BMTK to read. to change this, specify the config after the `plot` command. Eg:
```
bmtool plot --config simulation-config-23.json [FUNCTION]
```
## Ploting Connections
All connection tools can be customized by supplying additional arguments.
```
Options:
--title TEXT change the plot's title
--save-file TEXT save plot to path supplied
--sources TEXT comma separated list of source node types [default:all]
--targets TEXT comma separated list of target node types [default:all]
--sids TEXT comma separated list of source node identifiers
[default:node_type_id]
--tids TEXT comma separated list of target node identifiers
[default:node_type_id]
--no-prepend-pop When set don't prepend the population name to the unique
ids [default:False]
```
#### `--sources` and `--targets`
Are supplied as comma separated lists and corrospond with the population name specified in your model. Eg:
```
#initialize the networks in build_network.py
net = NetworkBuilder('hippocampus')
exp0net = NetworkBuilder('exp0input')
```
Default behavior is to plot connections between all populations but you can specify only a few to simplify your plots.
#### `--sids` and `--tids`
Comma separated lists of node identifiers replace the default `cell_id` automatically given to a cell population by BMTK. Any parameter passed to `NetworkBuilder.add_nodes` is stored in network `.h5` files and can be used to identify cells while connecting or producing plots. Eg:
```
# Adding nodes in build_network.py
net.add_nodes(N=inpTotal, pop_name='EC',
positions=p_EC,
model_type='biophysical',
model_template='hoc:IzhiCell_EC2',
morphology='blank.swc'
)
```
We could then use the pop_name to alter the output of our connection plots.
```
bmtool plot connection --sids pop_name --tids pop_name [FUNCTION]
```
#### `--no-prepend-pop`
Default behavior of bmtools is to print the population name before the cell id (or sid/tid) followed by an underscore. Eg: `hippocampus_100`. By supplying `--no-prepend-pop` the cell name becomes `100` unless specified otherwise.
#### `All together`
Using these optional switches we can see the difference in our plot output below.
```
bmtool plot connection total
```
vs.
```
bmtool plot connection --sources hippocampus --targets hippocampus --sids pop_name --tids pop_name --no-prepend-pop --title 'Hippocampus Total Connections' total
```
### Plot Total Connections
To plot the total number of connections between two populations of cells run
```
bmtool plot connection total
```
Remember to customize the output using the instructions above.
#### `--synfo`
This is an additional flag that can be used in the total connections plot. By default it is set to '0' which plots total connections.
If it is specified as '1', it plots the mean and standard deviation number of connections. If it is '2', it plots the .mod files used for that connection type.
Finally if it is '3', it plots the parameter file (.json) used for the connection.
### Plot Average Convergence/Divergence
To plot the average convergence or divergence of a single cell excute one of the following commands:
```
bmtool plot connection convergence
bmtool plot connection divergence
Add --method (std, min, or max) for additional function
```
### Plot Connection Diagram
To plot a rough sketch of cell type connectivity and the type of synapse used between cells run:
```
bmtool plot connection network-graph
```
`--edge-property` is an option available to change the synapse name if supplied to `NetworkBuilder.add_edges` when building the network. Default: `model_template`
### Edge Property Histograms
To view the distribution of an edge property between cell types run:
```
bmtool plot connection property-histogram-matrix
```
The following figure was generated using
```
bmtool plot connection --sources hippocampus --targets hippocampus --sids pop_name --tids pop_name --no-prepend-pop --title 'Synaptic Weight Distribution between Cell Types' property-histogram-matrix
```
By default the `property-histogram-matrix` looks at the `syn_weight` value specified in the `NetworkBuilder.add_edges` function when building your network. You can change this by specifying the `--edge-property`. Eg:
```
bmtool plot connection property-histogram-matrix --edge-property [PROPERTY]
```
#### Plotting edge values during/after runtime
BMTools is capable of plotting connection properties obtained after runtime from reports. This is useful for synaptic weights that change over time.
First, you must explicitly record the connection property in your `simulation_config.json`
```
"reports": {
"syn_report": {
"cells": "hippocampus",
"variable_name": "W_nmda",
"module": "netcon_report",
"sections": "soma",
"syn_type": "pyr2pyr",
"file_name": "syns.h5"
}
}
```
Where `pyr2pyr` is the `POINT_PROCESS` name for the synapse you're attempting to record, and the `variable_name` is a `RANGE` variable listed int the `NEURON` block of the synapse `.mod` file.
Once the simulation has been run un the following referencing the report specified above:
```
bmtool plot connection property-histogram-matrix --edge-property pyr2pyr_w --report output/syns.h5 --time 9999
```
The `--time-compare` option can be be used to show the weight distribution change between the specified times. Eg: ` --time 0 --time-compare 10000`
See the [BMTK Commit](https://github.com/AllenInstitute/bmtk/pull/67/files) for more details.
### Plotting Distance Probability Matrix between cell types
To show the probability of a cell type being connected to another cell type based on distance run:
```
bmtool plot connection prob
```
Full summary of options:
```
> bmtool plot connection prob --help
Usage: bmtool plot connection prob [OPTIONS]
Probabilities for a connection between given populations. Distance and
type dependent
Options:
--axis TEXT comma separated list of axis to use for distance measure eg:
x,y,z or x,y
--bins TEXT number of bins to separate distances into (resolution) -
default: 8
--line Create a line plot instead of a binned bar plot
--verbose Print plot values for use in another script
--help Show this message and exit.
```
A more complete command (used for image above) may look similar to
```
bmtools plot connection --sources hippocampus --targets hippocampus --no-prepend-pop --sids pop_name --tids pop_name prob --bins 10 --line --verbose
```
This will plot cells in the `hippocampus` network, using the `pop_name` as the cell identifier. There will be `10` bins created to group the cell distances. A `line` plot will be generated instead of the default `bar` chart. All values for each plot will be printed to the console due to the `verbose` flag.
All `point_process` cell types will be ignored since they do not have physical locations.
### Plotting Current Clamp and Spike Train Info
To plot all current clamp info involved in a simulation, use the following command (uses 'simulation_config.json' as default)
```
bmtools plot --config simulation_config_foo.json iclamp
```
To plot all spike trains and their target cells,
```
bmtools plot --config simulation_config_foo.json input
```
### Printing basic cell information involved in a simulation
```
bmtools plot --config simulation_config_foo.json cells
```
### Simulation Summary
Using previous functions, plots connection probability as a function of distance, total connections, cell information, current clamp information, input spike train information, and a 3D plot of the network if specified.
```
bmtools plot --config simulation_config_foo.json summary
```
## Cell Tuning
### Single Cell Tuning
From a BMTK Model directory containing a `simulation_config.json` file:
```
bmtools util cell tune --builder
```
For non-BMTK cell tuning:
```
bmtools util cell --template TemplateFile.hoc --mod-folder ./ tune --builder
```
### FIR Curve plotting
```
> bmtools util cell fi --help
Usage: bmtools util cell fi [OPTIONS]
Creates a NEURON GUI window with FI curve and passive properties
Options:
--title TEXT
--min-pa INTEGER Min pA for injection
--max-pa INTEGER Max pA for injection
--increment FLOAT Increment the injection by [i] pA
--tstart INTEGER Injection start time
--tdur INTEGER Duration of injection default:1000ms
--advanced Interactive dialog to select injection and recording
points
--help Show this message and exit.
> bmtools util cell fi
? Select a cell: (Use arrow keys)
» CA3PyramidalCell
DGCell
IzhiCell
IzhiCell_BC
IzhiCell_EC
IzhiCell_EC2
IzhiCell_EC_BIO
IzhiCell_EmoExcitatory
IzhiCell_EmoInhibitory
IzhiCell_OLM
IzhiCell_int
```
### VHalf Segregation Module
Based on the Alturki et al. (2016) paper.
Segregate your channel activation for an easier time tuning your cells.
```
> bmtools util cell vhseg --help
Usage: bmtools util cell vhseg [OPTIONS]
Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify
tuning by separating channel activation
Options:
--title TEXT
--tstop INTEGER
--outhoc TEXT Specify the file you want the modified cell template
written to
--outfolder TEXT Specify the directory you want the modified cell
template and mod files written to (default: _seg)
--outappend Append out instead of overwriting (default: False)
--debug Print all debug statements
--fminpa INTEGER Starting FI Curve amps (default: 0)
--fmaxpa INTEGER Ending FI Curve amps (default: 1000)
--fincrement INTEGER Increment the FI Curve amps by supplied pA (default:
100)
--infvars TEXT Specify the inf variables to plot, skips the wizard.
(Comma separated, eg: inf_mech,minf_mech2,ninf_mech2)
--segvars TEXT Specify the segregation variables to globally set,
skips the wizard. (Comma separated, eg:
mseg_mech,nseg_mech2)
--eleak TEXT Specify the eleak var manually
--gleak TEXT Specify the gleak var manually
--othersec TEXT Specify other sections that a window should be
generated for (Comma separated, eg: dend[0],dend[1])
--help Show this message and exit.
```
#### Examples
Wizard Mode (Interactive)
```
> bmtool util cell vhseg
? Select a cell: CA3PyramidalCell
Using section dend[0]
? Show other sections? (default: No) Yes
? Select other sections (space bar to select): done (2 selections)
? Select inf variables to plot (space bar to select): done (5 selections)
? Select segregation variables [OR VARIABLES YOU WANT TO CHANGE ON ALL SEGMENTS at the same time] (space bar to select): done (2 selections)
```
Command Mode (Non-interactive)
```
bmtool util cell --template CA3PyramidalCell vhseg --othersec dend[0],dend[1] --infvars inf_im --segvars gbar_im --gleak gl_ichan2CA3 --eleak el_ichan2CA3
```
Example:
Simple models can utilize
```
bmtool util cell --hoc cell_template.hoc vhsegbuild --build
bmtool util cell --hoc segmented_template.hoc vhsegbuild
```
ex: [https://github.com/tjbanks/two-cell-hco](https://github.com/tjbanks/two-cell-hco)
## Planned future features
```
bmtools build
Create a starting point network
Download sample networks
bmtools plot
Plot variable traces
Plot spike rasters
X Plot cell positions
X Plot connection matricies
bmtools debug
X list cell types available for single debug
X Run a single cell in the network
Isolate a single cell in the network
```
نیازمندی
| مقدار | نام |
|---|---|
| - | bmtk |
| - | click |
| - | clint |
| - | h5py |
| - | matplotlib |
| - | networkx |
| - | numpy |
| - | pandas |
| - | questionary |
| - | pynmodlt |
نحوه نصب
نصب پکیج whl bmtool-0.2.3:
pip install bmtool-0.2.3.whl
نصب پکیج tar.gz bmtool-0.2.3:
pip install bmtool-0.2.3.tar.gz