Visualizaiton and Output
The core calculation produces output files consisting of tabular data where the first column is the time and subsequent columns are the values of whtever recorders are configured in the model. For a simple model there is just one output data set. For parameter sweeps (RunSet) there is one for each paramter value. Each data set is stored in two formats: a compact binary form with the .dat extension, and a space delimited text form with the .txt extension.
After the core calculation has finished, the results are summarized on an HTML page. The ViewConfig object exists to add plots to that page by defining some default views of the data. The normal usage is to embed a ViewConfig block within the main model file containing one or more plot definition. Currently the available plots are: LineGraph, MeanVariance and PowerSpectrum as described below. All three plot definitions have the same structure. The LineGraph just produces plots of the columns of the specified output file against time. The other plot types perform some processing on the data first and plot the derived data on appropriate axes. The MeanVariance plot is a special case for performing mean-variance analysis and is only useful if the data it is given are currents from a single compartment with a single type of stochastic ion channel.
The contents of a LineGraph block are optional axis definitions, one or more Line or LineSet definitions, and one or more View definitions. The Line and LineSet blocks work the same way to specify the file that the data comes from, and optionally the line width, color etc. The View blocks each define a single plot of the data, specifying the axis ranges for the view window.
The data that is plotted does not have to come from the results of the PSICS calculation. Other data filed can be included in the folder and plotted the same way, as long as they conform to plain ascii table structure. For the case where different units were used for external files, the data can be rescaled by setting the rescale parameterin a LineSet definition.
One last convenience element in a LineGraph definition is the DataComparison block. This also referes to a reference file, but instead of generating a plot, the mean mean and variance of the difference between the plotted data and the comparison data will be computed and added to the html output file.
ViewConfig |
Default visualization definitions |
within: PSICSRun |
Postprocessing and visualization to be run on output data
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| morphology | Flag | Set to false to suppress creating morphology plots | "true" or "yes", "false" or "no" | ||
| morphologyData | Flag | Set to true to export the morphology data so it can be plotted independently | "true" or "yes", "false" or "no" |
Elements
| Element type | Role |
|---|---|
| LineGraph, PowerSpectrum, MeanVariance | Plot families. Each plot family may contain multiple views with different axis ranges |
| Raster | Rasters |
LineGraph |
A plot of recorder values against time |
within: ViewConfig |
This is the standard plot type for PSICS output. It should contain specifications of one or more data sources, one or more views and optional axis definitions.
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| width | Whole number | default width for plots | (100, 800) | ||
| height | Whole number | default height for plots | (100, 600) |
Elements
| Element type | Role |
|---|---|
| LineSet, Line | Data sources |
| View | Views of the data |
| XAxis
(max 1 instance) | default x axis range and label |
| YAxis
(max 1 instance) | default y axis range and label |
XAxis |
X axis label and default range |
within: LineGraph |
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| min | Floating point value | lower limit | none | () | |
| max | Floating point value | upper limit | none | () | |
| label | plain text | axis label | |||
Elements - No child elements are allowed
YAxis |
Y axis label and default range |
within: LineGraph |
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| min | Floating point value | lower limit | none | () | |
| max | Floating point value | upper limit | none | () | |
| label | plain text | axis label | |||
Elements - No child elements are allowed
Line |
within: LineGraph |
A single line specified by two columns from a file
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| file | text - the path to the file or folder | The name of the file containing the data | yes | ||
| width | Floating point value | width for plotting lines | none | (0.5, 10) | |
| show | Whole number | If set, shows just the specified column from the file | |||
| maxshow | Whole number | limits the number of lines plotted from the file, defaulting to 20 if not specified | (1, 100) | ||
| color | plain text | Color to plot the data in | Either one of the recognized color names (red, green, blue, magenta, cyan etc) or a hex color such as #ff0000 (which would give red) | ||
| rescale | plain text | Optional rescaling to make the axes of the data match other items in the plot | This is primarily for reference data from external sources. If the units used in the reference data are differnt from those generated by psics, it can be rescaled by setting this to a two element vector. For example, the value '[1, 1000]]' will cause the data from the first column to be used as is, but the second column will be multiplied by 1000 before plotting. This would be needed, for example, if the reference data was in Volts and was to be compared with PSICS output in milliVolts. | ||
| label | plain text | label to go in key | The label to use in the key. If it is not set, the line will be labelled with the file name | ||
| function | plain text | Plot a function of the data rather than the points themselves. | Currently this can only take the single value 'mean' to have the mean of all the columns plotted. | ||
Elements
| Element type | Role |
|---|---|
| DataComparison | optional comparisons with reference data |
| Stats | optional comparisons with reference data |
LineSet |
the data that goes into a plot |
within: LineGraph |
A set of lines defining data to be plotted. The default representation is to plot columns 1 throuhg N from the specified file against the first column, where N is either the last column in the file, or the value of the maxshow attribute, if set
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| file | text - the path to the file or folder | The name of the file containing the data | yes | ||
| width | Floating point value | width for plotting lines | none | (0.5, 10) | |
| show | Whole number | If set, shows just the specified column from the file | |||
| maxshow | Whole number | limits the number of lines plotted from the file, defaulting to 20 if not specified | (1, 100) | ||
| color | plain text | Color to plot the data in | Either one of the recognized color names (red, green, blue, magenta, cyan etc) or a hex color such as #ff0000 (which would give red) | ||
| rescale | plain text | Optional rescaling to make the axes of the data match other items in the plot | This is primarily for reference data from external sources. If the units used in the reference data are differnt from those generated by psics, it can be rescaled by setting this to a two element vector. For example, the value '[1, 1000]]' will cause the data from the first column to be used as is, but the second column will be multiplied by 1000 before plotting. This would be needed, for example, if the reference data was in Volts and was to be compared with PSICS output in milliVolts. | ||
| label | plain text | label to go in key | The label to use in the key. If it is not set, the line will be labelled with the file name | ||
| function | plain text | Plot a function of the data rather than the points themselves. | Currently this can only take the single value 'mean' to have the mean of all the columns plotted. | ||
Elements
| Element type | Role |
|---|---|
| DataComparison | optional comparisons with reference data |
| Stats | optional comparisons with reference data |
View |
A view on the data |
within: LineGraph |
Defines the axis ranges for a plot
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| id | identifier | ID for this view - the ids should be unique within a ViewConfig definition | yes | ||
| xmin | Floating point value | lower value of X axis | none | () | |
| xmax | Floating point value | upper value of X axis | none | () | |
| ymin | Floating point value | lower value of Y axis | none | () | |
| ymax | Floating point value | upper value of Y axis | none | () |
Elements - No child elements are allowed
Stats |
Simple statistics |
within: LineGraph |
Calculate simple statistics of result data
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| xmin | Floating point value | ms | |||
| xmax | Floating point value | ms |
Elements - No child elements are allowed
PowerSpectrum |
Power spectrum plot |
within: ViewConfig |
Like the MeanVariance component, this has all the properties of a normal LineSet, but instead of plotting hte data directly, it computes the PSD and plots that.
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| file | text - the path to the file or folder | The name of the file containing the data | yes | ||
| width | Floating point value | width for plotting lines | none | (0.5, 10) | |
| show | Whole number | If set, shows just the specified column from the file | |||
| maxshow | Whole number | limits the number of lines plotted from the file, defaulting to 20 if not specified | (1, 100) | ||
| loglog | Flag | Returns log10(f) and log10(psd) | "true" or "yes", "false" or "no" | ||
| color | plain text | Color to plot the data in | Either one of the recognized color names (red, green, blue, magenta, cyan etc) or a hex color such as #ff0000 (which would give red) | ||
| rescale | plain text | Optional rescaling to make the axes of the data match other items in the plot | This is primarily for reference data from external sources. If the units used in the reference data are differnt from those generated by psics, it can be rescaled by setting this to a two element vector. For example, the value '[1, 1000]]' will cause the data from the first column to be used as is, but the second column will be multiplied by 1000 before plotting. This would be needed, for example, if the reference data was in Volts and was to be compared with PSICS output in milliVolts. | ||
| label | plain text | label to go in key | The label to use in the key. If it is not set, the line will be labelled with the file name | ||
| function | plain text | Plot a function of the data rather than the points themselves. | Currently this can only take the single value 'mean' to have the mean of all the columns plotted. | ||
Elements
| Element type | Role |
|---|---|
| DataComparison | optional comparisons with reference data |
| Stats | optional comparisons with reference data |
MeanVariance |
Plot of variance against mean |
within: ViewConfig |
Mean-variance analysis of data. This includes all the parameters of a LineSet, but instead of plotting the raw data, it computes the mean and varianceover the given time window and plots the variance against the mean
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| file | text - the path to the file or folder | The name of the file containing the data | yes | ||
| tmin | Floating point value | Lower bound of region of interest | none | (0,) | |
| tmax | Floating point value | Upper bound of region of interest | none | (0,) | |
| binSize | Floating point value | Bin size for means | none | (0,) | |
| width | Floating point value | width for plotting lines | none | (0.5, 10) | |
| show | Whole number | If set, shows just the specified column from the file | |||
| maxshow | Whole number | limits the number of lines plotted from the file, defaulting to 20 if not specified | (1, 100) | ||
| color | plain text | Color to plot the data in | Either one of the recognized color names (red, green, blue, magenta, cyan etc) or a hex color such as #ff0000 (which would give red) | ||
| rescale | plain text | Optional rescaling to make the axes of the data match other items in the plot | This is primarily for reference data from external sources. If the units used in the reference data are differnt from those generated by psics, it can be rescaled by setting this to a two element vector. For example, the value '[1, 1000]]' will cause the data from the first column to be used as is, but the second column will be multiplied by 1000 before plotting. This would be needed, for example, if the reference data was in Volts and was to be compared with PSICS output in milliVolts. | ||
| label | plain text | label to go in key | The label to use in the key. If it is not set, the line will be labelled with the file name | ||
| function | plain text | Plot a function of the data rather than the points themselves. | Currently this can only take the single value 'mean' to have the mean of all the columns plotted. | ||
Elements
| Element type | Role |
|---|---|
| DataComparison | optional comparisons with reference data |
| Stats | optional comparisons with reference data |
| Comparison
(max 1 instance) | Optional theoretical values for comparison |
Comparison |
Theoretical curve for a MeanVariance plot |
within: MeanVariance |
Comparison model for mean variance analysis. Based on the supplied single channel conductance and number of channels it generates the expected variance at for a range of values of the mean. Only applicable within a MeanVariance plot
Attributes
| Name | Type | Definition | Units | Range | Required |
|---|---|---|---|---|---|
| iSingle | Floating point value | single channel conductance | none | (0,) | |
| nChannel | Whole number | number of channels | (0,) |
Elements - No child elements are allowed