def savePlots(self, results=None):
""" Store png images of the plots to be used as images, """
# Add resmap libraries to the path
sys.path.append(os.environ['RESMAP_HOME'])
# This is needed right now because we are having
# some memory problem with matplotlib plots right now in web
Plotter.setBackend('Agg')
self._plotVolumeSlices().savefig(self._getExtraPath('volume1.map.png'))
plot = self._plotResMapSlices(results['resTOTALma'])
plot.savefig(self._getExtraPath('volume1_resmap.map.png'))
self._plotHistogram().savefig(self._getExtraPath('histogram.png'))
def main():
parser = argparse.ArgumentParser(prog='Scipion Plot')
parser.add_argument('--file', help='File to visualize', required=True)
parser.add_argument('--block', help='Block to visualize')
parser.add_argument('--type', help='Plot type')
parser.add_argument('--columns', help='Columns to plot')
parser.add_argument('--xcolumn', help='X Column to plot')
parser.add_argument('--orderColumn', help='Column to order')
parser.add_argument('--orderDir', help='Order direction(ASC, DESC)')
parser.add_argument('--bins',
help='If plot type is histogram, number of bins')
parser.add_argument('--colors', help='Colors to plot columns')
parser.add_argument('--styles', help='Styles to plot columns')
parser.add_argument('--markers', help='Markers to plot columns')
parser.add_argument('--title', help='Plot title', default='')
parser.add_argument('--ytitle', help='Y axis title', default='')
parser.add_argument('--xtitle', help='X axis title', default='')
args = parser.parse_args()
plotfile = args.file
block = args.block if args.block else ''
type = args.type
columns = args.columns
xcolumn = args.xcolumn
orderColumn = args.orderColumn
orderDir = args.orderDir
bins = args.bins
colors = args.colors
styles = args.styles
markers = args.markers
title = args.title
xtitle = args.xtitle
ytitle = args.ytitle
Plotter.setBackend('TkAgg')
plotter = EmPlotter.createFromFile(plotfile, block, type, columns, colors,
styles, markers, xcolumn, ytitle,
xtitle, title, bins, orderColumn,
orderDir)
plotter.show(block=True)
def main():
parser = argparse.ArgumentParser(prog='Scipion Plot')
parser.add_argument('--file', help='File to visualize', required=True)
parser.add_argument('--block', help='Block to visualize')
parser.add_argument('--type', help='Plot type')
parser.add_argument('--columns', help='Columns to plot')
parser.add_argument('--xcolumn', help='X Column to plot')
parser.add_argument('--orderColumn', help='Column to order')
parser.add_argument('--orderDir', help='Order direction(ASC, DESC)')
parser.add_argument('--bins', help='If plot type is histogram, number of bins')
parser.add_argument('--colors', help='Colors to plot columns')
parser.add_argument('--styles', help='Styles to plot columns')
parser.add_argument('--markers', help='Markers to plot columns')
parser.add_argument('--title', help='Plot title', default='')
parser.add_argument('--ytitle', help='Y axis title', default='')
parser.add_argument('--xtitle', help='X axis title', default='')
args = parser.parse_args()
#print args
plotfile = args.file
block = args.block if args.block else ''
type = args.type
columns = args.columns
xcolumn = args.xcolumn
orderColumn = args.orderColumn
orderDir = args.orderDir
bins = args.bins
colors = args.colors
styles = args.styles
markers = args.markers
title = args.title
xtitle = args.xtitle
ytitle = args.ytitle
Plotter.setBackend('TkAgg')
plotFile(plotfile, block, type,
columns, colors, styles, markers,
xcolumn, ytitle, xtitle, title, bins, orderColumn, orderDir).show(block=True)
def __init__(self, path, master=None):
# Load global configuration
self.projName = os.path.basename(path)
try:
projTitle = '%s (%s on %s)' % (self.projName,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
projTitle = self.projName
self.projPath = path
self.project = self.loadProject()
# TODO: put the menu part more nicely. From here:
menu = MenuConfig()
projMenu = menu.addSubMenu('Project')
projMenu.addSubMenu('Browse files',
'browse',
icon='fa-folder-open.gif')
projMenu.addSubMenu('Remove temporary files',
'delete',
icon='fa-trash-o.gif')
projMenu.addSubMenu('Manage project labels', 'labels', icon=Icon.TAGS)
projMenu.addSubMenu('Toggle color mode',
'color_mode',
shortCut="Ctrl+t",
icon=Icon.ACTION_VISUALIZE)
projMenu.addSubMenu('Select all protocols',
'select all',
shortCut="Ctrl+a")
projMenu.addSubMenu('Find protocol to add',
'find protocol',
shortCut="Ctrl+f")
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Import workflow',
'load_workflow',
icon='fa-download.gif')
projMenu.addSubMenu('Search workflow',
'search_workflow',
icon='fa-search.gif')
if pw.Config.debugOn():
projMenu.addSubMenu('Export tree graph', 'export_tree')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Debug Mode',
'debug mode',
shortCut="Ctrl+d",
icon='debug.gif')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Notes', 'notes', icon='fa-pencil.gif')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Exit', 'exit', icon='fa-sign-out.gif')
helpMenu = menu.addSubMenu('Help')
helpMenu.addSubMenu('Online help',
'online_help',
icon='fa-external-link.gif')
helpMenu.addSubMenu('About', 'about', icon='fa-question-circle.gif')
helpMenu.addSubMenu('Contact support',
'contact_us',
icon='fa-question-circle.gif')
self.menuCfg = menu
if self.project.openedAsReadOnly():
self.projName += "<READ ONLY>"
# Notify about the workflow in this project
self.selectedProtocol = None
self.showGraph = False
Plotter.setBackend('TkAgg')
ProjectBaseWindow.__init__(self,
projTitle,
master,
minsize=(90, 50),
icon=Icon.SCIPION_ICON_PROJ)
OS.handler().maximizeWindow(self.root)
self.switchView(VIEW_PROTOCOLS)
self.initProjectTCPServer(
) # Socket thread to communicate with clients
ProjectWorkflowNotifier(self.project).notifyWorkflow()
def __init__(self, path, master=None):
# Load global configuration
self.projName = os.path.basename(path)
try:
projTitle = '%s (%s on %s)' % (self.projName,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
projTitle = self.projName
self.projPath = path
self.loadProject()
# TODO: put the menu part more nicely. From here:
menu = MenuConfig()
projMenu = menu.addSubMenu('Project')
projMenu.addSubMenu('Browse files', 'browse',
icon='fa-folder-open.png')
projMenu.addSubMenu('Remove temporary files', 'delete',
icon='fa-trash-o.png')
projMenu.addSubMenu('Manage project labels', 'labels',
icon=Icon.TAGS)
projMenu.addSubMenu('Toogle color mode', 'color_mode',
shortCut="Ctrl+t", icon=Icon.ACTION_VISUALIZE)
projMenu.addSubMenu('Select all protocols', 'select all',
shortCut="Ctrl+a")
projMenu.addSubMenu('Find protocol to add', 'find protocol',
shortCut="Ctrl+f")
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Import workflow', 'load_workflow',
icon='fa-download.png')
projMenu.addSubMenu('Search workflow', 'search_workflow',
icon = 'fa-search.png')
projMenu.addSubMenu('Export tree graph', 'export_tree')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Notes', 'notes', icon='fa-pencil.png')
projMenu.addSubMenu('', '') # add separator
projMenu.addSubMenu('Exit', 'exit', icon='fa-sign-out.png')
helpMenu = menu.addSubMenu('Help')
helpMenu.addSubMenu('Online help', 'online_help',
icon='fa-external-link.png')
helpMenu.addSubMenu('About', 'about',
icon='fa-question-circle.png')
helpMenu.addSubMenu('Contact support', 'contact_us',
icon='fa-question-circle.png')
self.menuCfg = menu
# TODO: up to here
if self.project.openedAsReadOnly():
self.projName += "<READ ONLY>"
# Notify about the workflow in this project
self.icon = self.generalCfg.icon.get()
self.selectedProtocol = None
self.showGraph = False
Plotter.setBackend('TkAgg')
ProjectBaseWindow.__init__(self, projTitle, master,
icon=self.icon, minsize=(90,50))
self.root.attributes("-zoomed", True)
self.switchView(VIEW_PROTOCOLS)
self.initProjectTCPServer() # Socket thread to communicate with clients
ProjectWorkflowNotifier(self.project).notifyWorkflow()
