Commit 74c42755 authored by Gael Goret's avatar Gael Goret
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......@@ -49,20 +49,53 @@ context, MDANCE GUI can now be considered as an interactive graphical environmen
development and the integration of of the components necessary for implementing new analysis.
3.1] An Interactive Graphical Environment
One of the main features that MDANCE offer is the possibility to visualize and interact with 3D graphics. Thanks to developments based on wxPython[ref] and the visualization toolkit libraries[ref], it is possible to display a molecular trajectory, pick a set of atoms, or interpret simply 2D or 3D resulting data as 3D density plot, elevated surface, scalar field... The MDANCE graphical environment allow to navigate interactively from the input of data, going through the parameterization of analyses to the visualization of results in an user friendly and integrated way. However, being a python package, MDANCE can also be accessed through the command line interface.
Working Environment
The main window is divided in four panels (numbered from 1 to 4 on figure 1). The first panel is the MDANCE workspace where all the actions will take place via a drag and drop mechanism of data and their related actions (e.g. viewing a molecule, trajectory animation, launching a job …). The second panel is the data panel that will display all the data that have been loaded in the current MDANCE session. Dragging a data from this panel and dropping it on the workspace will create a tab that will serve as a container for all subsequent actions related to this data. Dropping an action on this tab will automatically pop up its related GUI (widget, dialog, viewer …). The third panel is the plugins panel that will contains all the actions related to the widget currently on focus into the workspace. This panel is dynamically updated each time the user selects a widget on the workspace. For example, a typical workflow for MDANCE would be the following. 1) The user loads a trajectory. It is displayed in the data panel. 2) Data is dragged and dropped into the workspace. That creates a tab in the workspace waiting for further actions which are displayed in the plugins panel. 3) The user drags and drops the molecular viewer plugin into the previously created tab. The molecular viewer widget pops up in the tab showing the molecular contents of the trajectory. 4) The user animates the trajectory by dragging and dropping the animation panel into the previously created molecular viewer. And so on. Finally, the fourth panel contains various widgets related to the current MDANCE session. It contains 1) a logger of the application. 2) a python console, allowing to handle the MDANCE frameworks interactively. 3) a job manager, showing the states of the running jobs.
3.2] 2D/3D Plotter
In the workflow of MDANCE, once an analyses has finished, a NetCDF file containing the results is written. To interpret properly this content, we have provided an integrated tool adapted to all the dimensions of the output data. Based respectively on matplotlib and VTK for 2D and 3D rendering, the MDANCE plotter produces publication quality figures for the classic rendering types. The 1D and 2D data can be plotted as lines and images in single or multiple windows. To enhance the possibility cross comparison, the units conversions are handle automatically, and slices coming from different images can be merged into the same plot easily. For data with higher dimensionality several plotting modes can be used (1) the image elevation mode (see figure 2) displays 2D data as 3D colored landscape, (2) the scalar-field mode displays 3D densities as a field of combined gradient of color and transparency, (3) the iso-surface mode is another way to plot 3D densities represented in that case as a transparent surface going through all the values with the same intensity (see figure 3). This plotter includes also the possibility of slicing the density using a cut plan interpolating the data.
One of the main features that MDANCE offer is the possibility to visualize and interact with 3D graphics.
Thanks to developments based on wxPython[ref] and the visualization toolkit libraries[ref], it is possible to display a molecular trajectory,
pick a set of atoms, or interpret simply 2D or 3D resulting data as 3D density plot, elevated surface, scalar field...
The MDANCE graphical environment allow to navigate interactively from the input of data, going through the parameterization of analyses
to the visualization of results in an user friendly and integrated way. However, being a python package, MDANCE can also be accessed
through the command line interface.
3.2]Working Environment
The main window is divided in four panels (numbered from 1 to 4 on figure 1). The first panel is the MDANCE workspace where all the actions will
take place via a drag and drop mechanism of data and their related actions (e.g. viewing a molecule, trajectory animation, launching a job …).
The second panel is the data panel that will display all the data that have been loaded in the current MDANCE session. Dragging a data from this panel
and dropping it on the workspace will create a tab that will serve as a container for all subsequent actions related to this data.
Dropping an action on this tab will automatically pop up its related GUI (widget, dialog, viewer …). The third panel is the plugins panel that will
contains all the actions related to the widget currently on focus into the workspace. This panel is dynamically updated each time the user selects
a widget on the workspace. For example, a typical workflow for MDANCE would be the following. 1) The user loads a trajectory.
It is displayed in the data panel. 2) Data is dragged and dropped into the workspace. That creates a tab in the workspace waiting for further actions
which are displayed in the plugins panel. 3) The user drags and drops the molecular viewer plugin into the previously created tab.
The molecular viewer widget pops up in the tab showing the molecular contents of the trajectory. 4) The user animates the trajectory by
dragging and dropping the animation panel into the previously created molecular viewer. And so on. Finally, the fourth panel contains
various widgets related to the current MDANCE session. It contains 1) a logger of the application. 2) a python console, allowing to handle the
MDANCE frameworks interactively. 3) a job manager, showing the states of the running jobs.
3.3] 2D/3D Plotter
In the workflow of MDANCE, once an analyses has finished, a NetCDF file containing the results is written.
To interpret properly this content, we have provided an integrated tool adapted to all the dimensions of the output data.
Based respectively on matplotlib and VTK for 2D and 3D rendering, the MDANCE plotter produces publication quality figures for the
classic rendering types. The 1D and 2D data can be plotted as lines and images in single or multiple windows. To enhance the possibility
cross comparison, the units conversions are handle automatically, and slices coming from different images can be merged into the same plot easily.
For data with higher dimensionality several plotting modes can be used (1) the image elevation mode (see figure 2) displays 2D data as
3D colored landscape, (2) the scalar-field mode displays 3D densities as a field of combined gradient of color and transparency, (3) the iso-surface
mode is another way to plot 3D densities represented in that case as a transparent surface going through all the values with
the same intensity (see figure 3). This plotter includes also the possibility of slicing the density using a cut plan interpolating the data.
Figure 1.]
Snapshot of MDANCE main window with the different panels of the working environment numbered from 1 to 4.
3.3] Properties Editor
Most of the quantities proposed by MDANCE can be weighted by using specific properties (atomic masses and numbers, coherent and incoherent scattering lengths, etc.). in MDANCE the list of those properties is easily extensible, which open the use of MDANCE to new experimental techniques (e.g. X-ray scattering, infrared and RMN spectroscopy). Thereby, in MDANCE the properties editor expose the modification of the elements data base which allow the users to tune freely the weighting scheme (see figure 4).
This properties editor displays the MDANCE elements database. It is editable which allows the management of the atomic properties of all defined atoms. Additionally, new atom types can be added, in order to fit some special molecular dynamics simulations. For instance, when computing analyses related to neutron spectrometry, some hydrogen atoms should be turned to deuterium to match the experience. In such case, the use of properties editor will allow to add the deuterium as a new entry and to further transmute some of the hydrogen atoms into deuterium.
3.4] Properties Editor
Most of the quantities proposed by MDANCE can be weighted by using specific properties (atomic masses and numbers, coherent and
incoherent scattering lengths, etc.). in MDANCE the list of those properties is easily extensible, which open the use of MDANCE to new
experimental techniques (e.g. X-ray scattering, infrared and RMN spectroscopy). Thereby, in MDANCE the properties editor expose the
modification of the elements data base which allow the users to tune freely the weighting scheme (see figure 4).
This properties editor displays the MDANCE elements database. It is editable which allows the management of the atomic properties
of all defined atoms. Additionally, new atom types can be added, in order to fit some special molecular dynamics simulations.
For instance, when computing analyses related to neutron spectrometry, some hydrogen atoms should be turned to deuterium to match the
experience. In such case, the use of properties editor will allow to add the deuterium as a new entry and to further transmute some of
the hydrogen atoms into deuterium.
Figure 4.]
The MDANCE properties editor which gives access to the MDANCE elements database.
......@@ -73,9 +106,15 @@ An elevation plot produced by MDANCE plotting tool.
Figure 3.]
An elevation plot produced by MDANCE plotting tool.
3.4] An Extendable Framework
MDANCE has been structured in such a way that user can extend easily most of the principal software components. Indeed, the MDANCE framework is based on a set of interfaces for which each base class is metaclassed in order to provide the (automatic) self-registration into a tree like structure called Registry at import time. Each branch of this tree will store the classes that compose each of these interfaces (e.g. Jobs, Configurators, Plugins …) and will be built up only when it will be required in the course of the execution flow.
This object-oriented design provides some flexibility for any user that would like to extend any of these interfaces. Indeed, he /she will just have to subclass any of their base class and MDANCE will take in charge their automatic registration at runtime. This also allows, thanks to the introspection mechanism to transparently integrate in MDANCE the user made component derived from the base classes identically as if they were built-in components. The figure 5 shows all the programming interfaces that are handled by the registry.
3.5] An Extendable Framework
MDANCE has been structured in such a way that user can extend easily most of the principal software components. Indeed, the MDANCE framework
is based on a set of interfaces for which each base class is metaclassed in order to provide the (automatic) self-registration into a tree like
structure called Registry at import time. Each branch of this tree will store the classes that compose each of these interfaces (e.g. Jobs,
Configurators, Plugins …) and will be built up only when it will be required in the course of the execution flow.
This object-oriented design provides some flexibility for any user that would like to extend any of these interfaces.
Indeed, he /she will just have to subclass any of their base class and MDANCE will take in charge their automatic registration at runtime.
This also allows, thanks to the introspection mechanism to transparently integrate in MDANCE the user made component derived from the base
classes identically as if they were built-in components. The figure 5 shows all the programming interfaces that are handled by the registry.
Figure 5.]
The MDANCE extendable components handled by the class registry.
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