Welcome to h5xplorer’s documentation!¶

h5xplorer is a modular interface for the vizualization of data stored in HDF5 files. Not only the defalut menu allows you to quickly plot the dataset stored in your hdf5 files but you can quickly create new menu items specfic to your dta and the way you want to visualize it !!! OMG !!!

Installation¶

The code is hosted on GitHub (https://github.com/DeepRank/h5xplorer)

To install the code:

clone the repository git clone https://github.com/DeepRank/h5xplorer
go there cd h5xplorer
install pip install -e ./

Tutorial : The simplest app¶

h5xplorer allows to create an app very quickly thanks to default context menu that are automatically used if nothing else is specified. In a new file enters.

>>> #!/usr/bin/env python
>>> from h5xplorer.h5xplorer import h5xplorer
>>> app = h5xplorer()

Execute this file and you’ll be able to explore our hdf5 file. The default menu is executed in the background. The default menu file teaches us how t build our own context menu. Let’s look at it

>>> from PyQt5 import QtWidgets
>>> from h5xplorer.menu_tools import *
>>> from h5xplorer.menu_plot import *
>>>
>>> def default_context_menu(self, treeview, position):
>>>
>>>     """Generate a right-click menu for the items"""
>>>
>>>     all_item = get_current_item(self,treeview,single=False)
>>>
>>>     if len(all_item) == 1:
>>>
>>>         item = all_item[0]
>>>         data = get_group_data(get_current_hdf5_group(self,item))
>>>
>>>         if data is None:
>>>             list_operations = ['Print attrs']
>>>
>>>         elif data.ndim == 1:
>>>             list_operations = ['Print attrs','-','Plot Hist', 'Plot Line']
>>>
>>>         elif data.ndim == 2:
>>>             list_operations = ['Print attrs','-','Plot Hist', 'Plot Map']
>>>
>>>         else:
>>>             list_operations = ['Print attrs']
>>>
>>>         action,actions = get_actions(treeview,position,list_operations)
>>>
>>>         if action == actions['Print attrs']:
>>>             send_dict_to_console(self,item,treeview)
>>>
>>>         if 'Plot Hist' in actions:
>>>             if action == actions['Plot Hist']:
>>>                 plot_histogram(self,item,treeview)
>>>
>>>         if 'Plot Line' in actions:
>>>             if action == actions['Plot Line']:
>>>                 plot_line(self,item,treeview)
>>>
>>>         if 'Plot Map' in actions:
>>>             if action == actions['Plot Map']:
>>>                 plot2d(self,item,treeview)
>>>
>>>     elif len(all_item) == 2:
>>>
>>>         item0,item1 = all_item
>>>
>>>         list_operations = ['Plot Scatter','Plot Line']
>>>         action,actions = get_actions(treeview,position,list_operations)
>>>
>>>         if action == actions['Plot Scatter']:
>>>             plot1D(self,item0,item1,treeview,plot='scatter')
>>>
>>>         if action == actions['Plot Line']:
>>>             plot1D(self,item0,item1,treeview,plot='line')

Tutorial : A bit more advanced then¶

Documentation¶

All the prototypes of the class/methods are here specified

Get items¶

Some functionalities are preimplemented to access the items and stuff

h5xplorer.menu_tools.get_current_item(self, treeview, single=False)[source]¶

Get the item(s) that was selected

Parameters:	treeview (HDF5TreeWidget) – the treeview single (bool, optional) – if true only single item possible
Returns:	Description
Return type:	TYPE

h5xplorer.menu_tools.get_current_hdf5_group(self, item)[source]¶

Get the HDF5 group of the selected item

Parameters:	item (HDF5TreeItem) – treeview item
Returns:	the corresponding group
Return type:	HDF5 group

h5xplorer.menu_tools.get_group_data(group)[source]¶

Get the dataset of the item

Parameters:	group (HDF5 group) – group of the treeview item
Returns:	return np.array if the group has a dataset or None otherwise
Return type:	dataset or None

h5xplorer.menu_tools.get_actions(treeview, position, list_action)[source]¶

Generate a singlelevel context menu of action and return the selected one

Example:

>>> list_operations = ['Print attrs','-','Plot Hist', 'Plot Map']
>>> action,actions = get_actions(treeview,position,list_operations)
>>> if action == actions['Print attrs']:
        send_dict_to_console(self,item,treeview)

Parameters:	treeview (HDF5TreeWidget) – the treeview position (TYPE) – Description list_action (list) – List of string giving the action names
Returns:	dict of QTMenu actions actions: the selected action
Return type:	actions

h5xplorer.menu_tools.get_multilevel_actions(treeview, position, list_action, sub_list)[source]¶

Generate a multilevel context menu of action and return the selected one

Example:

>>> list_operations = ['Hit Rate','Av. Prec.']
>>> list_subop = [['Train','Valid','Test'],['Train','Valid','Test']]
>>> action,actions = get_multilevel_actions(treeview,position,list_operations,list_subop)

Parameters:	treeview (HDF5TreeWidget) – the treeview position (TYPE) – Description list_action (list) – List of string giving the action names sub_list (list) – list of string giving the subactions
Returns:	dict of QTMenu actions actions: the selected action
Return type:	actions

h5xplorer.menu_tools.send_dict_to_console(self, item, treeview)[source]¶

Send a dictionany to the QT console

Parameters:	item (HDF5TreeItem) – treeview item treeview (HDF5TreeWidget) – the treeview

h5xplorer.menu_tools.print_attributes(self, item, treeview)[source]¶

Print the attribute in the console

Parameters:	item (HDF5TreeItem) – treeview item treeview (HDF5TreeWidget) – the treeview

h5xplorer.menu_tools.get_user_values(varnames, vartypes='float', windowtitle='Enter Values')[source]¶

Get the values of variables from the users

Parameters:	varnames (list) – list of strings of all the desired variables windowtitle (str, optional) – Name of the window
Returns:	list of float of the desired variables
Return type:	list

Plotting routines¶

Some functionalities are preimplemented to plot dataset in the QT console

h5xplorer.menu_plot.plot_histogram(self, item, treeview, nbins=10)[source]¶

Plot an histogram of the data

Example:

>>> def context_menu(self,treeview,position):
>>>     all_item = get_current_item(self,treeview,single=False)
>>>     item = all_item[0]
>>>     list_operations = ['Plot Hist']
>>>     action,actions = get_actions(treeview,position,list_operations)
>>>     if action == actions['Plot Hist']:
            plot_histogram(self,item,treeview)

Parameters:	item (HDF5TreeItem) – treeview item treeview (HDF5TreeWidget) – treeview nbins (int, optional) – number of bins in the histogram

h5xplorer.menu_plot.plot_line(self, item, treeview)[source]¶

Plot a line plot of a single item VS its index

Example:

>>> def context_menu(self,treeview,position):
>>>     all_item = get_current_item(self,treeview,single=False)
>>>     item = all_item[0]
>>>     list_operations = ['Plot Line']
>>>     action,actions = get_actions(treeview,position,list_operations)
>>>     if action == actions['Plot Line']:
            plot_line(self,item,treeview)

Parameters:	item (HDF5TreeItem) – treeview item treeview (HDF5TreeWidget) – treeview

h5xplorer.menu_plot.plot1D(self, item0, item1, treeview, plot='line')[source]¶

Plot a XY line or scatter plot of two items

Note: You must be able to select multiple items to use this method. So you must create the app with:

>>> app = h5xplorer(extended_selection=True)

Example:

>>> def context_menu(self,treeview,position):
>>>     all_item = get_current_item(self,treeview,single=False)
>>>     item0 = all_item[0]
>>>     item1 = all_item[1]
>>>     list_operations = ['Plot1D']
>>>     action,actions = get_actions(treeview,position,list_operations)
>>>     if action == actions['Plot1D']:
            plot1D(self,item0,item1,treeview)

Parameters:	item0 (HDF5TreeItem) – treeview item for the X data item1 (HDF5TreeItem) – treeview item for the Y data treeview (HDF5TreeWidget) – treeview plot (str, optional) – ‘line’ or ‘scatter’

h5xplorer.menu_plot.plot2d(self, item, treeview)[source]¶

Plot a map of a 2D data array

Example:

>>> def context_menu(self,treeview,position):
>>>     all_item = get_current_item(self,treeview,single=False)
>>>     item = all_item[0]
>>>     list_operations = ['Plot2D']
>>>     action,actions = get_actions(treeview,position,list_operations)
>>>     if action == actions['Plot2D']:
            plot2D(self,item,treeview)

Parameters:	item (HDF5TreeItem) – treeview item treeview (HDF5TreeWidget) – treeview

Core design of the app¶

classes and stuff that the app is built from

Core App¶

class h5xplorer.h5xplorer.DummyHDF5Group(dictionary, attrs={}, name='DummyHDF5Group')[source]¶

Bases: dict

Dummy HDF5 group created sometimes ….

Parameters:	dictionary (dict) – attrs (dict, optional) – name (str, optional) – Name of the group

file = None¶

parent = None¶

class h5xplorer.h5xplorer.HDF5TreeItem(data_file, parent, name, row)[source]¶

Bases: object

Create a new item for an HDF5 tree

Parameters:	data_file (HDF5 data file) – This is the file (NB must be the top-level group) containing everything parent (HDF5TreeItem) – The parent of the current item name (string) – The name of the current item (should be parent.name plus an extra component) row (int) – The index of the current item in the parent’s children.

basename¶

has_children¶

children¶

purge_children()[source]¶: Empty the cached list of children.

h5item¶: The underlying HDF5 item for this tree item.

class h5xplorer.h5xplorer.h5xplorer(func_menu=<function default_context_menu>, baseimport=None, extended_selection=False)[source]¶

Bases: object

cleanup()[source]¶

Welcome to h5xplorer’s documentation!¶

Installation¶

Tutorial : The simplest app¶

Tutorial : A bit more advanced then¶

Documentation¶

Get items¶

Plotting routines¶

Core design of the app¶

Core App¶

Dialog box¶

Indices and tables¶