mxcube / blissframework Goto Github PK

**DEPRECATED**: BlissFramework is now part of mxcube repository

Python 63.10% CSS 1.02% JavaScript 21.96% HTML 13.92%

blissframework's Introduction

MXCuBE

MXCuBE stands for Macromolecular Xtallography Customized Beamline Environment. The project started in 2005 at ESRF, since then it has been adopted by other institutes in Europe. In 2010, a collaboration agreement has been signed for the development of MXCuBE with the following partners:

Latest information about the MXCuBE project can be found in the project webpage.

MXCuBE is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

MXCuBE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with MXCuBE. If not, see https://www.gnu.org/licenses/.

Information for developers

Information for users

User Manual MXCuBE3
User manual MXCuBE2.
Feature overview
Overview of Graphical user interface
If you cite MXCuBE, please use the references:

Oscarsson, M. et al. 2019. “MXCuBE2: The Dawn of MXCuBE Collaboration.” Journal of Synchrotron Radiation 26 (Pt 2): 393–405.

Gabadinho, J. et al. (2010). MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments. J. Synchrotron Rad. 17, 700-707

blissframework's People

Contributors

Stargazers

Watchers

Forkers

hellmig ivarskarpics maxlabmx olofsvensson lgadea douglasbeniz rhfogh soleilpx2 yongmeibian

blissframework's Issues

Store gui file in yaml

Store gui file in yaml format

MXCuBE (Qt4) crashes when loading gui_config_file (on 'task_tollbox_brick')

I am starting a brand new installation, all repositories cloned from master. When I try to run MXCuBE the program it bombs out before the gui starts, giving the message below. Full details at the bottom of this issue. Can anyone help?

[...]

[...]

File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 305, in make_connections
getattr(sender, connection["signal"]).connect(slot)
AttributeError: 'NullBrick' object has no attribute 'request_tree_brick'
QObject::startTimer: QTimer can only be used with threads started with QThread
2017-02-09 17:05:05,172 |HWR |INFO | XML-RPC server closed

There are previous error messages because PyMca is not installed, but this should not be relevant (?).

The precise command being run is:
'~/pycharm/MXCuBE2/mxcube-2/bin/mxcube --hardwareRepository ~/pycharm/MXCuBE2/mxcube-2/ExampleFiles/HardwareObjects.xml/'

The versions of the various libraries are:
|~> conda env export -n mxpath
name: mxpath
channels: !!python/tuple

!!python/unicode
'defaults'
dependencies:
cairo=1.12.18=0
dateutil=2.4.1=py27_0
freetype=2.4.10=0
gevent=1.2.0=py27_0
greenlet=0.4.11=py27_0
libgfortran=1.0=0
libpng=1.5.13=1
matplotlib=1.3.1=np18py27_1
numpy=1.8.2=py27_1
openssl=1.0.2j=0
pip=9.0.1=py27_1
pixman=0.26.2=0
py2cairo=1.10.0=py27_2
pydispatcher=2.0.5=py27_0
pyparsing=2.0.1=py27_0
pyqt=4.10.4=py27_0
python=2.7.13=0
pytz=2016.10=py27_0
qt=4.8.5=0
readline=6.2=2
scipy=0.14.0=np18py27_0
setuptools=27.2.0=py27_0
sip=4.15.5=py27_0
six=1.10.0=py27_0
sqlite=3.13.0=0
tk=8.5.18=0
wheel=0.29.0=py27_0
zlib=1.2.8=3
pip:
- py4j==0.10.4
- python-dateutil==2.4.1

The full log message is:
|> mxcube
Using PyQt: PyQt4
qt version: 4.8.5 / pyqt version: 4.10.4
Matplotlib version: 1.3.1
Matplotlib is COMPATIBLE with PyQt
Using PyQt: PyQt4
qt version: 4.8.5 / pyqt version: 4.10.4
Matplotlib version: 1.3.1
Matplotlib is COMPATIBLE with PyQt
2017-02-09 17:05:02,413 |root |INFO | =================================================================================
2017-02-09 17:05:02,413 |root |INFO | Starting MXCuBE v2.3
2017-02-09 17:05:02,413 |root |INFO | Qt4 GUI file: /home/rhfogh/pycharm/MXCuBE2/mxcube-2/example_mxcube_qt4.gui
2017-02-09 17:05:02,413 |root |INFO | Hardware repository: /home/rhfogh/pycharm/MXCuBE2/mxcube-2/ExampleFiles/HardwareObjects.xml/
2017-02-09 17:05:02,416 |root |INFO | System info: Python 2.7.13 on Linux
2017-02-09 17:05:02,416 |root |INFO | - Qt 4.8.5 - PyQt4 4.10.4
2017-02-09 17:05:02,416 |root |INFO | - Matplotlib 1.3.1 -
2017-02-09 17:05:02,416 |root |INFO | ---------------------------------------------------------------------------------
2017-02-09 17:05:02,432 |root |INFO | Connected to Hardware Repository server ['/home/rhfogh/pycharm/MXCuBE2/mxcube-2/ExampleFiles/HardwareObjects.xml/']
2017-02-09 17:05:02,543 |HWR |DEBUG | LDAP Server is not available
2017-02-09 17:05:03,685 |root |WARNING| Could not find autocentring library, automatic centring is disabled
2017-02-09 17:05:03,709 |HWR |DEBUG | Diffractometer: Camera hwobj is not defined
2017-02-09 17:05:03,709 |HWR |DEBUG | Diffractometer: Adding phi motor to centring motors
2017-02-09 17:05:03,710 |HWR |WARNING| Diffractometer: Motor phiz listed in the centring motor list, but not initalized
2017-02-09 17:05:03,710 |HWR |WARNING| Diffractometer: Motor phiy listed in the centring motor list, but not initalized
2017-02-09 17:05:03,710 |HWR |WARNING| Diffractometer: Motor sampx listed in the centring motor list, but not initalized
2017-02-09 17:05:03,711 |HWR |WARNING| Diffractometer: Motor sampy listed in the centring motor list, but not initalized
2017-02-09 17:05:03,711 |HWR |DEBUG | Diffractometer: Adding kappa motor to centring motors
2017-02-09 17:05:03,711 |HWR |DEBUG | Diffractometer: Adding kappa_phi motor to centring motors
2017-02-09 17:05:03,712 |HWR |WARNING| Diffractometer: Motor beam_x listed in the centring motor list, but not initalized
2017-02-09 17:05:03,712 |HWR |WARNING| Diffractometer: Motor beam_y listed in the centring motor list, but not initalized
2017-02-09 17:05:03,712 |HWR |WARNING| Diffractometer: Sample Changer is not defined
2017-02-09 17:05:03,712 |HWR |WARNING| Diffractometer: Neither zoom centre nor camera size iz defined
2017-02-09 17:05:03,811 |HWR |INFO | SampleChanger: Using update timer is True
2017-02-09 17:05:03,823 |HWR |INFO | SampleChanger: Using update timer is True
2017-02-09 17:05:03,824 |root |INFO | connectNotify stateChanged
2017-02-09 17:05:03,824 |root |INFO | connectNotify infoChanged
2017-02-09 17:05:03,824 |root |INFO | connectNotify statusChanged
2017-02-09 17:05:03,824 |root |INFO | connectNotify stateChanged
2017-02-09 17:05:03,825 |root |INFO | connectNotify infoChanged
2017-02-09 17:05:03,825 |GUI |INFO | Data collection is enabled
('@@', ('fourier', 8000), <class SimpleXMLRPCServer.SimpleXMLRPCRequestHandler at 0x7fbe01eca188>, 2, 1)
@@~ about to bind
('@@ server_bind', True, ('fourier', 8000), ('0.0.0.0', 0))
@@ about to bind
('@@ bound', ('192.168.131.112', 8000))
@@ about to activate
2017-02-09 17:05:03,905 |HWR |INFO | XML-RPC server listening on: fourier:8000
2017-02-09 17:05:03,905 |HWR |INFO | Registering functions in module Native with XML-RPC server
2017-02-09 17:05:03,915 |HWR |INFO | Registering function Native.queue_add_child as XML-RPC function queue_add_child
2017-02-09 17:05:03,915 |HWR |INFO | Registering function Native.queue_add_node as XML-RPC function queue_add_node
2017-02-09 17:05:03,915 |HWR |INFO | Registering function Native.queue_get_available_serialisations as XML-RPC function queue_get_available_serialisations
2017-02-09 17:05:03,915 |HWR |INFO | Registering function Native.queue_get_model_code as XML-RPC function queue_get_model_code
2017-02-09 17:05:03,916 |HWR |INFO | Registering function Native.queue_get_node as XML-RPC function queue_get_node
2017-02-09 17:05:03,916 |HWR |INFO | Registering function Native.queue_get_serialisation as XML-RPC function queue_get_serialisation
2017-02-09 17:05:03,916 |HWR |INFO | Registering function Native.queue_set_serialisation as XML-RPC function queue_set_serialisation
2017-02-09 17:05:03,916 |HWR |INFO | Registering function Native.queue_update_result as XML-RPC function queue_update_result
2017-02-09 17:05:03,924 |root |INFO | connectNotify progressInit
2017-02-09 17:05:03,924 |root |INFO | connectNotify progressStep
2017-02-09 17:05:03,924 |root |INFO | connectNotify progressStop
2017-02-09 17:05:04,192 |root |ERROR | Cannot import module Qt4_TaskToolBoxBrick
Traceback (most recent call last):
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_Configuration.py", line 38, in loadModule
mod = imp.load_module(brick_name, fp, path_name, description)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/Qt4_TaskToolBoxBrick.py", line 29, in
from widgets.Qt4_task_toolbox_widget import TaskToolBoxWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_task_toolbox_widget.py", line 32, in
from widgets.Qt4_create_energy_scan_widget import CreateEnergyScanWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_create_energy_scan_widget.py", line 33, in
from Qt4_periodic_table_widget import PeriodicTableWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_periodic_table_widget.py", line 27, in
from PyMca import QPeriodicTable
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
ImportError: No module named PyMca
2017-02-09 17:05:04,193 |root |ERROR | Cannot load brick task_tollbox_brick : module could not be loaded.
2017-02-09 17:05:04,393 |root |INFO | connectNotify statusChanged
2017-02-09 17:05:04,394 |root |INFO | connectNotify stateChanged
2017-02-09 17:05:04,394 |root |INFO | connectNotify infoChanged
2017-02-09 17:05:04,394 |root |INFO | connectNotify selectionChanged
2017-02-09 17:05:04,394 |root |INFO | connectNotify loadedSampleChanged
2017-02-09 17:05:04,562 |root |ERROR | Cannot import module Qt4_EnergyScanParametersBrick
Traceback (most recent call last):
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_Configuration.py", line 38, in loadModule
mod = imp.load_module(brick_name, fp, path_name, description)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/Qt4_EnergyScanParametersBrick.py", line 23, in
from widgets.Qt4_energy_scan_parameters_widget import EnergyScanParametersWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_energy_scan_parameters_widget.py", line 25, in
from widgets.Qt4_periodic_table_widget import PeriodicTableWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_periodic_table_widget.py", line 27, in
from PyMca import QPeriodicTable
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
ImportError: No module named PyMca
2017-02-09 17:05:04,562 |root |ERROR | Cannot load brick energy_scan_brick : module could not be loaded.
2017-02-09 17:05:04,582 |root |ERROR | Cannot import module Qt4_XRFSpectrumParametersBrick
Traceback (most recent call last):
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_Configuration.py", line 38, in loadModule
mod = imp.load_module(brick_name, fp, path_name, description)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/Qt4_XRFSpectrumParametersBrick.py", line 23, in
from widgets.Qt4_xrf_spectrum_parameters_widget import XRFSpectrumParametersWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_xrf_spectrum_parameters_widget.py", line 26, in
from widgets.Qt4_mca_spectrum_widget import McaSpectrumWidget
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/Bricks/widgets/Qt4_mca_spectrum_widget.py", line 54, in
from PyMca import McaAdvancedFit
File "/home/rhfogh/Software/Miniconda2/envs/mxpath/lib/python2.7/site-packages/gevent/builtins.py", line 93, in import
result = _import(*args, **kwargs)
ImportError: No module named PyMca
2017-02-09 17:05:04,583 |root |ERROR | Cannot load brick xrf_spectrum_parameters : module could not be loaded.
2017-02-09 17:05:04,682 |root |INFO | connectNotify infoChanged
2017-02-09 17:05:04,753 |HWR |WARNING| pdfkit not available
2017-02-09 17:05:04,754 |HWR |DEBUG | BeamlineTest: directory for test reports not defined. Set to: /tmp/mxcube/beamline_test
2017-02-09 17:05:04,808 |HWR |ERROR | Cannot load Hardware Object "/" : file not found.
2017-02-09 17:05:04,865 |root |INFO | HUTCH IS CLOSED, YOU ARE ALLOWED TO TAKE CONTROL AGAIN
2017-02-09 17:05:04,920 |root |INFO | connectNotify statusChanged
2017-02-09 17:05:04,920 |root |INFO | connectNotify stateChanged
2017-02-09 17:05:04,920 |root |INFO | connectNotify infoChanged
2017-02-09 17:05:04,920 |root |INFO | connectNotify selectionChanged
2017-02-09 17:05:04,921 |root |INFO | connectNotify loadedSampleChanged
2017-02-09 17:05:05,012 |root |ERROR | No slot 'logged_in' in receiver task_tollbox_brick
2017-02-09 17:05:05,012 |root |ERROR | No slot 'set_session' in receiver task_tollbox_brick
2017-02-09 17:05:05,012 |root |ERROR | No slot 'user_group_saved' in receiver task_tollbox_brick
2017-02-09 17:05:05,012 |root |ERROR | No slot 'selection_changed' in receiver task_tollbox_brick
2017-02-09 17:05:05,012 |root |ERROR | No slot 'populate_parameter_widget' in receiver energy_scan_brick
2017-02-09 17:05:05,013 |root |ERROR | No slot 'populate_xrf_widget' in receiver xrf_spectrum_parameters
2017-02-09 17:05:05,013 |root |ERROR | No slot 'set_tree_brick' in receiver task_tollbox_brick
2017-02-09 17:05:05,013 |root |ERROR | exception while loading GUI file
Traceback (most recent call last):
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 412, in finish_init
main_widget = self.load_gui(gui_config_file)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 233, in load_gui
main_window = self.execute(self.configuration)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 312, in execute
make_connections(config.windows_list)
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 309, in make_connections
make_connections(item["children"])
File "/home/rhfogh/pycharm/MXCuBE2/mxcube-2/BlissFramework/Qt4_GUISupervisor.py", line 305, in make_connections
getattr(sender, connection["signal"]).connect(slot)
AttributeError: 'NullBrick' object has no attribute 'request_tree_brick'
QObject::startTimer: QTimer can only be used with threads started with QThread
2017-02-09 17:05:05,172 |HWR |INFO | XML-RPC server closed

Code cleanup (summer cleaning)

Hi all,

I did a major code clean up of the BlissFramework code and now it is much closer to PEP guidelines.
During the cleanup I found also some bugs and removed lots of not used code.
Please update to the latest master version and inform me if there is any problems.

Added comment to the widgets properties

Hi all,

I added comments to the widget properties. Now when adding a new property it is possible to add a comment. For example:

self.addProperty('diskThreshold', 'float', 200, comment='Disk threshold')
self.addProperty('maxPlotPoints', 'integer', 100, comment="Maximal number of plot points")
self.addProperty('showDiskSize', 'boolean', True, comment="Display information about disk size")

On the property table a comment will be displayed like:

As you can see now properties are divided in two tables. If the property starts with "hwobj_" it is displayed in the second table.

Python 3 support

Hi all,

Few weeks around there was a workaround to test if it is possible to use mxcube and python3. With a major help from @douglasbeniz the initial work was done and MXCuBE is compatible with python3.x. There will be coming more commits (also to HardwareRepository) and bug fixes.

Cheers,
Ivars

Add prefixes to properties that initiate hwobj

Add prefix hwob_ to properties that indicate hwobjs

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.