Usage

The Menus

“File”

‘Open’

Select a PATCHMASTER or PATCHMASTER NEXT .dat file. (Alternatively, you can open a file by dragging it onto the PMbrowser window. Non-bundled files, which consist of a collection of various files, usually .pul and .pgf and possibly others are also present.)

‘Close’

Close currently open file.

‘Export…’ Submenu

Here you find options to export traces (available export formats: .pxp, and .ibw for import by IgorPro, numpy format .npy for import by python, and raw binary data) and metadata as a table.

When exporting traces and the choosen file format does not support inclusion of metadata, for each trace a .json file will be created that contains the exported metadata.

all visible traces

All traces that are currently visible (i.e. not hidden) in the tree-view are selected for export. Traces can be hidden either by filtering (see ‘Filter’ and ‘Tree-Filter’ Dialog) or by using the context menue of the tree-view.

selected with children

All visible traces, that are children of the node currently selected in the tree-view are selected for export. This function also available from the context menue of the tree-view (“export subtree”).

The export dialog will appear, which allows you to select paths and filenames as well as several options that pertain to exports to packed experiment files (also see Notes on Exporting Data for IgorPro for additional information on exports).

metadata as table

Export metadata as tab-delimited table. The table can be either copied to the clipboard or saved to file. Parameters marked for export (see ‘Select Parameters’ Dialog ) will be included in the export. In addition to these parameters, the first four columns of the table will contain the group, series, sweep, and trace counts. You can choose per which level of the pulse tree a table row should be produced.

You can decide if numbers should be formatted according to the system default. This is helpful if the table is to be imported into an application that expects such formatting, e.g. spreadsheet software.

Select Parameters

Opens the ‘Select Parameters’ Dialog. There you can select which parameters from the PatchMaster-file will be either printed to the text-area or exported as wave-notes and tables.

Preferences

Open Preferences dialog. Here you can configure how Imon and Vmon traces are labled.

“Edit”

‘Clear Text’

Clears the text-area.

“Tree”

‘Filter’

Allows you to hide unwanted nodes and traces from the tree-view, see ‘Tree-Filter’ Dialog.

‘Show All’

Un-hides all nodes and traces in the tree-view.

“Graph”

‘Auto Scale’

Set scaling of graph axes to extents of most recently loaded trace.

‘Do Autoscale on Load’

Toggle to enable or disable automatic scaling when a new trace is loaded into the graph. Also avaible from the context menue of the Graph Area.

‘YX mode (cur. trace as X)’

Enter YX mode. The currently selected trace will be used a X reference for subsequent drawing operations. This is especially usefull if you are working with ramp stimuli.

‘YT mode’

Enter YT mode, which is the default mode. Time will be used as the abscissa for the graph.

‘Wipe All’

Clear the Graph Area.

‘Wipe Background Traces’

Delete all displayed traces from the internal buffer of the graph. Only the current trace will remain visible in the graph area.

‘Settings and Ranges’

Opens dialog which allows altering certain settings of the graph area - see ‘Setting and Ranges’ Dialog.

“Help”

‘About’

Displays ‘About’-Dialog with various bits of information, including version of Qt-library against which the executable was build.

‘About Qt’

Displays dialog with information on Qt-library, including version of library actually used at runtime.

The Dialogs

Export data: ‘Choose Path & Prefix’ Dialog

Screenshot of Dialog Choose Path and Prefix

This dialog is displayed every time you are about to export traces.

General options

  • ‘path’ If multiple files are exported, this is the path they will be saved to. Use button ‘choose…’ to call up a file dialog to choose the path (or enter a valid path manually).

  • ‘prefix’ Exported waves will be prefixed with this text. If individual files are exported, they will have this prefix, too.

Selection of export method

All methods export additional metadata. See ‘Select Parameters’ Dialog for details on selection of parameters to be exported as metadata.

Note on multi-file exports from flatpaks

If you have installed PMbrowser as a flatpak, there is a caveat: Due to restrictions imposed by flatpak’s sandbox, export methods that produce multiple files can only be used within the Documents folder (or subfolders thereof). If you export to a single .pxp file, this restriction does not apply.

Export for Igor Pro

  • Checkbox ‘create pxp file’

    All waves will be exported into a single packaged experiment file (pxp). After clicking ‘OK’, a file dialog will show up that allows you to select a filename for the file to be created.

  • Checkbox ‘create folder structure’

    If you export as a pxp file, select this to create datafolders within the pxp file that match the tree structure. You can choose if the grouping level for traces should be group or series.

Metadata will be included as wavenotes.

Export NPY for Python / numpy + metadata as JSON

  • Checkbox ‘gather sweeps’

    If gather sweeps is not selected, each trace will be exported as a .npy file. Metadata for each trace will be export in JSON format (.json).

    If gather sweeps is selected, for each series that is about to be exported, all traces that are a (grand-)child of this series and that share the same trace ID will be gathered in a single .npy file as a 2D array. The first dimension of this array is the trace index, the second dimension the time (or x) dimension of the trace. This file will be accompanied by a JSON file containing the metadata for all sweeps/traces in the .npy file.

    If for example a series has 10 sweeps that are to be exported and each sweep has a Vmon and an Imon trace, for this series two files will be created. One contains the 10 Vmon traces, the other contains the 10 Imon traces.

.npy files can be read via numpy.load(<filename>). Demo python code showing how to use these files can be found in the Git repository (folder demo).

Export raw binary + metadata as JSON

Each trace will be export as a .bin raw binary file. The data is exported as 64bit floating point. Metadata for each trace, including samplerate, will be export in JSON format (.json).

‘Tree-Filter’ Dialog

This dialog allows you to hide nodes and traces of the data-tree that you are not interested in. It can be accessed from the Tree menu or via the Filter… button.

The filtering is based on perl style regular expressions. Only elements that match the given expression will remain visible, all other elements will be hidden.

The expression .* will match any name, therefore you can use it to display all nodes of a given category.

See section Selecting / Filtering Traces of Interest from the New User Tour for an example how to use this feature.

‘Select Parameters’ Dialog

For each of the four tree levels Group, Series, Sweep, and Trace you can select which parameters will be printed into the text area when a node is selected in the tree-view (checkbox ‘print’) and / or added to the wave-note of exported traces and exported as metadata tables (checkbox ‘export’, cf. section Notes on Exporting Data for IgorPro).

All paramters that might be of relevance should be available. If you miss something, please post a feature request on PMbrowser’s issues page.

Times can represented as relative times (Rel. time). The time reference for calculation of the relative times can be set using the context menu of the tree-view. By default, the reference time is the start time of the dat-file.

‘Setting and Ranges’ Dialog

Here you can configure the display area: axis ranges, autoscale on load, if grid lines should be displayed, colors used for drawing traces and grid and the number of overlay traces to be kept in the internal display buffer.