def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setWindowTitle(APPNAME)
self.setWindowFlags(Qt.Window | Qt.WindowContextHelpButtonHint |
Qt.WindowMinimizeButtonHint |
Qt.WindowMaximizeButtonHint |
Qt.WindowCloseButtonHint)
self.project = None
self.current_plugin = None
self.project_manager = ProjectManager(self)
self.plugins = self.load_plugins()
self.sidebar = Sidebar()
self.setup_ui()
self.setup_signals()
self.enable(False)
self.pipeline_model = PipelineModel()
self.sidebar.pl_list.setModel(self.pipeline_model)
self.pipeconf.pipeline_list.setModel(self.pipeline_model)
last = str(QSettings().value('path_of_last_project'))
if last:
quit_msg = "Load last project " + last + " ?"
reply = QMessageBox.question(self, 'Project Setup',
quit_msg, QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
if last:
try:
self.open_project(last)
except:
qtutil.critical('Previous project appears to have been corrupted.\n \n'
+ traceback.format_exc(), self)
#qtutil.critical("Previous project appears to have been corrupted. Please move or delete it.")
self.sidebar.setup_sidebar_values(self.project)
def insert_application(self, application):
application['created_time'] = datetime.now()
applier = dict(username=g.user['username'], name=g.user['name'])
application['applier'] = applier
application['status'] = 0
pm = ProjectManager()
apply_project = pm.find_project_by_id(application['project']['id'])
self.conn.projects.update_one(
{'_id': ObjectId(application['project']['id'])},
{
'$push': {
'appliers': applier
}
}
)
application['project']['name'] = apply_project['name']
result = self.conn.application.insert_one(application)
message = dict()
message['created_time'] = datetime.now()
message['receiver'] = apply_project['creator']['id']
message['sender'] = applier
message['type'] = 0
message['status'] = 0
message['attachment'] = dict(application=str(result.inserted_id))
self.conn.messages.insert_one(message)
return True
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setWindowTitle(APPNAME)
self.setWindowFlags(Qt.Window | Qt.WindowContextHelpButtonHint |
Qt.WindowMinimizeButtonHint |
Qt.WindowMaximizeButtonHint |
Qt.WindowCloseButtonHint)
self.project = None
self.current_plugin = None
self.project_manager = ProjectManager(self)
self.plugins = self.load_plugins()
self.sidebar = Sidebar()
self.setup_ui()
self.setup_signals()
self.enable(False)
self.pipeline_model = PipelineModel()
self.sidebar.pl_list.setModel(self.pipeline_model)
self.pipeconf.pipeline_list.setModel(self.pipeline_model)
last = str(QSettings().value('path_of_last_project'))
if last:
quit_msg = "Load last project " + last + " ?"
reply = QMessageBox.question(self, 'Project Setup',
quit_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
if last:
try:
self.open_project(last)
except:
qtutil.critical('Previous project appears to have been corrupted.\n \n'
+ traceback.format_exc(), self)
#qtutil.critical("Previous project appears to have been corrupted. Please move or delete it.")
self.sidebar.setup_sidebar_values(self.project)
def main(ctx):
if not is_internet_up():
print("Please check your intenet connection")
return
config = configparser.ConfigParser()
config.read('config.ini')
ctx.obj["github"] = Github(config["GITHUB"]["API"])
ctx.obj["todo_manager"] = TodoManager(config["TODOIST"]["API"])
ctx.obj["path"] = config["PATH"]
ctx.obj["project_manager"] = ProjectManager()
class MainWindow(QMainWindow):
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setWindowTitle(APPNAME)
self.setWindowFlags(Qt.Window | Qt.WindowContextHelpButtonHint
| Qt.WindowMinimizeButtonHint
| Qt.WindowMaximizeButtonHint
| Qt.WindowCloseButtonHint)
self.project = None
self.current_plugin = None
self.project_manager = ProjectManager(self)
self.plugins = self.load_plugins()
self.sidebar = Sidebar()
self.setup_ui()
self.setup_signals()
self.enable(False)
self.pipeline_model = PipelineModel()
self.sidebar.pl_list.setModel(self.pipeline_model)
self.pipeconf.pipeline_list.setModel(self.pipeline_model)
last = str(QSettings().value('path_of_last_project'))
if last:
quit_msg = "Load last project " + last + " ?"
reply = QMessageBox.question(self, 'Project Setup', quit_msg,
QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
if last:
try:
self.open_project(last)
except:
qtutil.critical(
'Previous project appears to have been corrupted.\n \n'
+ traceback.format_exc(), self)
#qtutil.critical("Previous project appears to have been corrupted. Please move or delete it.")
self.sidebar.setup_sidebar_values(self.project)
def load_plugins(self):
"""This just gets all the plugins (no reference to pipeline)"""
plugins = collections.OrderedDict()
filenames = [
f for f in sorted(os.listdir('plugins')) if f.endswith('.py')
]
for filename in filenames:
name, ext = os.path.splitext(filename)
p = self.load_plugin('plugins.' + name, None)
if p:
plugins[name] = p
return plugins
def load_plugin(self, module, plugin_position):
try:
m = importlib.import_module(module)
if not hasattr(m, 'MyPlugin'):
return None
p = m.MyPlugin(self.project, plugin_position)
# p.run()
except:
print('Failed to import \'{}\'.'.format(module))
raise
else:
return p
# def reset_pipeline_plugins(self, plugin_names):
# for i, plugin_name in enumerate(plugin_names):
# p = self.load_plugin('plugins.' + plugin_name, i)
# if p:
# self.plugins[plugin_name] = p
# if self.current_plugin:
# self.set_plugin(self.current_plugin, None)
def reload_pipeline_plugins(self):
for i, plugin_name in enumerate(
self.pipeline_model.get_plugin_names()):
p = self.load_plugin('plugins.' + plugin_name, i)
if p:
self.plugins[plugin_name] = p
# def set_x(val):
# self.sidebar.x_origin.setValue(val)
# def set_y(val):
# self.sidebar.y_origin.setValue(val)
# if plugin_name == 'set_coordinate_system':
# p.widget.x_origin_changed[float].connect(self.set_x)
# p.widget.y_origin_changed[float].connect(set_y)
if self.current_plugin:
self.set_plugin(self.current_plugin, None)
def setup_ui(self):
self.pipeconf = PipeconfDialog(self.plugins, self)
self.datadialog = DataDialog(self)
self.pl_frame = QFrame()
splitter = QSplitter(self)
self.enable = lambda yes: splitter.setEnabled(yes)
splitter.setHandleWidth(3)
splitter.setStyleSheet('QSplitter::handle {background: #cccccc;}')
splitter.addWidget(self.sidebar)
splitter.addWidget(self.pl_frame)
# splitter.setStretchFactor(0, 0)
# splitter.setStretchFactor(1, 1)
self.setCentralWidget(splitter)
self.menu = self.menuBar()
m = self.menu.addMenu('&File')
a = QAction('&New project', self)
a.setShortcut('Ctrl+N')
a.setStatusTip('Create new project')
a.triggered.connect(self.create_project)
m.addAction(a)
a = QAction('&Open project', self)
a.setShortcut('Ctrl+O')
a.setStatusTip('Open project')
a.triggered.connect(self.open_project)
m.addAction(a)
a = QAction("&Quit", self)
a.setShortcut("Ctrl+Q")
a.setStatusTip('Leave The App')
a.setIcon(QIcon('pics/quit.png'))
a.triggered.connect(self.close)
m.addAction(a)
about_action = QAction('&About ' + APPNAME, self)
about_action.setStatusTip('About ' + APPNAME)
about_action.triggered.connect(self.about)
about_action.setShortcut('F1')
whats_this_action = QWhatsThis.createAction(
QAction('&What\'s This?', self))
whats_this_action.setShortcut('Shift+F1')
m = self.menu.addMenu('&Project')
m.setEnabled(False)
a = QAction("&Close", self)
a.setStatusTip('Close project')
a.triggered.connect(self.close_project)
m.addAction(a)
a = QAction("&Reset All Plugin Parameters", self)
a.setStatusTip(
'This is useful if you experience JSON-related issues allowing for a clean slate'
)
a.triggered.connect(self.reset_all_params)
m.addAction(a)
self.project_menu = m
help_menu = self.menu.addMenu('&Help')
help_menu.addAction(about_action)
help_menu.addAction(whats_this_action)
def reset_all_params(self):
for plugin_position, p in enumerate(self.project.pipeline):
if p['name'] in self.plugins.keys():
plugin = self.plugins[p['name']]
if hasattr(plugin, 'widget'):
if hasattr(plugin.widget, 'setup_params'):
if not hasattr(plugin.widget, 'params'):
plugin.widget.params = self.project.pipeline[
plugin_position]
plugin.widget.project = self.project
plugin.widget.plugin_position = plugin_position
try:
plugin.widget.setup_params(reset=True)
except:
print("Failed to reset " + p['name'])
def setup_signals(self):
self.datadialog.reload_plugins.connect(self.reload_pipeline_plugins)
self.sidebar.open_pipeconf_requested.connect(self.open_pipeconf)
self.sidebar.open_datadialog_requested.connect(self.open_datadialog)
self.sidebar.automate_pipeline_requested.connect(
self.automate_pipeline)
self.sidebar.x_origin_changed[float].connect(
functools.partial(self.set_project_coordinate_system, 'x'))
self.sidebar.y_origin_changed[float].connect(
functools.partial(self.set_project_coordinate_system, 'y'))
self.sidebar.units_per_pixel_changed[float].connect(
functools.partial(self.set_project_coordinate_system,
'units_per_pixel'))
self.plugins['set_coordinate_system'].widget.x_origin_changed[
float].connect(
functools.partial(self.set_project_coordinate_system, 'x'))
self.plugins['set_coordinate_system'].widget.y_origin_changed[
float].connect(
functools.partial(self.set_project_coordinate_system, 'y'))
# todo: add signals from set_coordinate_system here
self.sidebar.pl_list.active_plugin_changed[str, int].connect(
self.set_plugin)
self.sidebar.pl_list.setModel(self.pipeconf.pipeline_list.model())
def set_project_coordinate_system(self, key, value):
#todo: add update for view
self.project['origin'] = list(self.project['origin'])
if key == 'x':
self.project['origin'][0] = value
self.project.save()
elif key == 'y':
self.project['origin'][1] = value
self.project.save()
elif key == 'units_per_pixel':
self.project['unit_per_pixel'] = value
self.project.save()
if self.current_plugin in self.plugins.keys():
self.plugins[self.current_plugin].widget.view.update()
def create_project(self):
project = self.project_manager.new_project()
if project:
self.load_project(project)
def load_project(self, project):
self.clean()
self.project = project
self.setWindowTitle(APPNAME + ' - ' + project.name)
self.enable(True)
self.project_menu.setEnabled(True)
QSettings().setValue('path_of_last_project', project.path)
pipeline = []
for plugin_dict in self.project.pipeline:
# include fix to update old versions to new format
try:
plugin_name = plugin_dict['name']
except:
attrs = json.load(open('../templates/mbeproject.json'))
pipeline_template = attrs['pipeline']
# pipeline_names = [p['name'] for p in pipeline_template]
# plugins = self.load_plugins()
# for plugin_name in pipeline_names:
# for plugin in plugins:
# if plugin == plugin_name:
# pipeline.append((plugin, plugins[plugin].name))
# break
QMessageBox.about(
self,
'Critical Error in pipeline. Manual Reset Recommended', """
<p>Please quit and replace the pipeline in your project JSON file with</p>
<p></p>
<td>%s</td>
<p>which can be copied from
<a href="https://github.com/Frikster/Mesoscale-Brain-Explorer/blob/master/templates/mbeproject.json">here</a></p>
<p>Only the pipeline section needs to be replaced</p>
""" % pipeline_template)
# qtutil.critical("Pipeline appears to be corrupt. "
# "Please replace your current pipeline in the JSON file with \n"
# " " + str(pipeline_template) + "which can be copied from \n" +
# < a href = "https://github.com/Frikster/Mesoscale-Brain-Explorer/issues" > here < / a > < / p >
# "https://github.com/Frikster/Mesoscale-Brain-Explorer/blob/master/templates/mbeproject.json")
return
for plugin in self.plugins:
if plugin == plugin_name:
pipeline.append((plugin, self.plugins[plugin].name))
break
self.pipeline_model.set_plugins(pipeline)
self.reload_pipeline_plugins()
self.sidebar.setup_sidebar_values(project)
# self.reset_pipeline_plugins([p[0] for p in pipeline])
def open_project(self, path=''):
project = self.project_manager.open_project(path)
if project:
self.load_project(project)
def close_project(self):
self.clean()
self.project = None
self.setWindowTitle(APPNAME)
self.project_menu.setEnabled(False)
self.enable(False)
def set_plugin(self, plugin_name, plugin_position):
p = self.load_plugin('plugins.' + str(plugin_name), plugin_position)
if not p:
return
self.current_plugin = plugin_name
self.plugins[plugin_name] = p
def set_x(val):
self.sidebar.x_origin.setValue(val)
def set_y(val):
self.sidebar.y_origin.setValue(val)
if plugin_name == 'set_coordinate_system':
p.widget.x_origin_changed[float].connect(set_x)
p.widget.y_origin_changed[float].connect(set_y)
lt = QVBoxLayout()
lt.addWidget(p.widget)
self.clean_plugin()
self.pl_frame.setLayout(lt)
# p.run()
def clean_plugin(self):
if self.pl_frame.layout():
clear_layout(self.pl_frame.layout())
QWidget().setLayout(self.pl_frame.layout())
def clean(self):
model = self.sidebar.pl_list.model()
if model:
model.clear()
self.clean_plugin()
def open_pipeconf(self):
self.pipeconf.exec_()
pipeline = self.pipeline_model.get_plugin_names()
self.project.set_pipeline(pipeline)
self.project.save()
def open_datadialog(self):
self.datadialog.update(self.project)
self.datadialog.exec_()
def automate_pipeline(self):
# order by index
ordered_q_model_indexes = sorted(
self.sidebar.pl_list.selectedIndexes(),
key=lambda x: x.row(),
reverse=False)
if not ordered_q_model_indexes:
qtutil.info(
"Select all the plugins you want to process through. Use shift or ctrl to select multiple"
)
import_plugin_indexes = [
ind for ind in range(len(ordered_q_model_indexes))
if self.plugins[ordered_q_model_indexes[ind].data(
Qt.UserRole)].name in constants.IMPORT_PLUGINS
]
if not import_plugin_indexes:
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected(
) # find the number of files outputted by the first plugin
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected()
if not p.check_ready_for_automation(number_of_outputs):
qtutil.critical(p.automation_error_message())
return
number_of_outputs = p.output_number_expected(
number_of_outputs) # find the number of outputs
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
input_paths = p.get_input_paths()
if not input_paths:
qtutil.critical(
"The first plugin in the pipeline does not have a set of input files selected"
)
return
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
ordered_q_model_indexes_segments = []
for i, import_ind in enumerate(import_plugin_indexes):
if i < len(import_plugin_indexes) - 1:
# ordered_q_model_indexes are the indices in the GUI.
# retrieve the indices from where this import plugin is (import_ind) to
# the index right before the next import plugin
ordered_q_model_indexes_segment = ordered_q_model_indexes[
import_ind:(import_plugin_indexes[i + 1])]
else:
ordered_q_model_indexes_segment = ordered_q_model_indexes[
import_ind:]
ordered_q_model_indexes_segments = ordered_q_model_indexes_segments + [
ordered_q_model_indexes_segment
]
import_paths = []
for i, ordered_q_model_indexes_segment in enumerate(
ordered_q_model_indexes_segments):
import_plugin = self.plugins[
ordered_q_model_indexes_segment[0].data(Qt.UserRole)]
qtutil.info(
"Please select all your files for the pipeline starting from import plugin "
+ str(i))
input_paths = import_plugin.get_input_paths()
import_paths = import_paths + [input_paths]
if not input_paths:
qtutil.critical(
"import plugin " + str(i) +
" in the pipeline does not have a set of input files selected"
)
return
# ensure all selected plugins are ready for automation
for i, ordered_q_model_indexes_segment in enumerate(
ordered_q_model_indexes_segments):
not_import_plugins = [
self.plugins[ordered_q_model_indexes_segment[j].data(
Qt.UserRole)]
for j in range(1, len(ordered_q_model_indexes_segment))
]
number_of_outputs = len(import_paths[i])
for not_import_plugin in not_import_plugins:
if not not_import_plugin.check_ready_for_automation(
number_of_outputs):
qtutil.critical(
not_import_plugin.automation_error_message())
return
number_of_outputs = not_import_plugin.output_number_expected(
number_of_outputs)
for i, ordered_q_model_indexes_segment in enumerate(
ordered_q_model_indexes_segments):
input_paths = import_paths[i]
for q_model_index in ordered_q_model_indexes_segment:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
# p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
# input_paths = p.get_input_paths()
# if not input_paths:
# qtutil.critical("The first plugin in the pipeline does not have a set of input files selected")
# return
#
# for q_model_index in ordered_q_model_indexes:
# p = self.plugins[q_model_index.data(Qt.UserRole)]
# output_paths = p.run(input_paths)
# input_paths = output_paths
# self.sidebar.pl_list.selectedIndexes()[0].data(Qt.UserRole)
#
# self.sidebar.pl_list.selectedIndexes()[0].row()
# self.sidebar.pl_list.model().data(self.sidebar.pl_list.selectedIndexes()[0])
def about(self):
author = 'Cornelis Dirk Haupt'
date = '2017'
QMessageBox.about(
self, 'About ' + APPNAME, """
<b>%s</b>
<p>An online readme, including user manual and developer tutorial can be found
<a href="https://github.com/Frikster/Mesoscale-Brain-Explorer">here</a></p>
<p>Use the "what's this" feature to click on any UI component and learn how to use it</p>
<p>Please submit any feature requests or issues
<a href="https://github.com/Frikster/Mesoscale-Brain-Explorer/issues">here</a></p>
<p></p>
<p><table border="0" width="150">
<tr>
<td>Author:</td>
<td>%s</td>
</tr>
<tr>
<td>Version:</td>
<td>%s</td>
</tr>
<tr>
<td>Date:</td>
<td>%s</td>
</tr>
</table></p>
""" % (APPNAME, author, VERSION, date))
kshift = (1,1,1), # grid centered at supercell L point
pseudos = ['Ge.pbe-kjpaw.UPF'], # PBE pseudopotential
system = T_system # the interstitial system
)
# link together the simulation cascade
# current relax gets structure from previous
if len(relaxations)>0: # if it exists
relax.depends(relaxations[-1],'structure')
#end if
relaxations.append(relax) # add relax simulation to the list
#end for
# perform the simulations
pm = ProjectManager() # start the project manager
pm.add_simulations(relaxations) # give it the relax calculations
pm.run_project() # run all the jobs
# analyze the results
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
print
print 'Relaxation results:'
print '-------------------'
print ' kgrid starting force max force # of cycles'
for ik in range(len(supercell_kgrids)):
conv_thr=1e-6, # convergence threshold
kgrid=kgrid, # supercell k-point grid
kshift=(1, 1, 1), # grid centered at supercell L point
pseudos=['Ge.pbe-kjpaw.UPF'], # PBE pseudopotential
system=T_system # the interstitial system
)
# link together the simulation cascade
# current relax gets structure from previous
if len(relaxations) > 0: # if it exists
relax.depends(relaxations[-1], 'structure')
#end if
relaxations.append(relax) # add relax simulation to the list
#end for
# perform the simulations
pm = ProjectManager() # start the project manager
pm.add_simulations(relaxations) # give it the relax calculations
pm.run_project() # run all the jobs
# analyze the results
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
print
print 'Relaxation results:'
print '-------------------'
print ' kgrid starting force max force # of cycles'
for ik in range(len(supercell_kgrids)):
kgrid = supercell_kgrids[ik]
relax = relaxations[ik]
from fastapi import Depends, FastAPI, HTTPException, BackgroundTasks
from starlette.responses import Response
from starlette.staticfiles import StaticFiles
from fastapi.security import HTTPBasic, HTTPBasicCredentials
from starlette.status import HTTP_401_UNAUTHORIZED
from io import BytesIO, open
import os
import json
from storage import Storage
from project import ProjectManager
from models import Project
storage = Storage()
project_manager = ProjectManager()
app = FastAPI()
# project
@app.get("/api/projects")
def list_projects():
return storage.list_buckets()
@app.get("/api/projects/{bucket_name}")
def project_details(bucket_name):
try:
data = storage.get_object(bucket_name, 'project.json')
return json.loads(data)
except:
files = []
substeps=3, # MC steps taken w/o computing E_local
samplesperthread=40 # No. of dmc walkers per thread
),
dmc( # dmc parameters
timestep=0.01, # dmc timestep (1/Ha)
warmupsteps=50, # No. of MC steps before data is collected
blocks=400, # No. of data blocks recorded in scalar.dat
steps=5, # No. of steps per block
nonlocalmoves=True # use Casula's T-moves
), # (retains variational principle for NLPP's)
],
# return a list or object containing simulations
return_list=False)
#the project manager monitors all runs
pm = ProjectManager()
# give it the simulation objects
pm.add_simulations(qsims.list())
# run all the simulations
pm.run_project()
# print out the total energy
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
# get the qmcpack analyzer object
# it contains all of the statistically analyzed data from the run
qa = qsims.qmc.load_analyzer_image()
# get the local energy from dmc.dat
le = qa.dmc[1].dmc.LocalEnergy # dmc series 1, dmc.dat, local energy
timestep = 0.01, # dmc timestep (1/Ha)
warmupsteps = 50, # No. of MC steps before data is collected
blocks = 400, # No. of data blocks recorded in scalar.dat
steps = 5, # No. of steps per block
nonlocalmoves = True # use Casula's T-moves
), # (retains variational principle for NLPP's)
],
# return a list or object containing simulations
return_list = False
)
#the project manager monitors all runs
pm = ProjectManager()
# give it the simulation objects
pm.add_simulations(qsims.list())
# run all the simulations
pm.run_project()
# print out the total energy
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
# get the qmcpack analyzer object
# it contains all of the statistically analyzed data from the run
qa = qsims.qmc.load_analyzer_image()
class MainWindow(QMainWindow):
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setWindowTitle(APPNAME)
self.setWindowFlags(Qt.Window | Qt.WindowContextHelpButtonHint |
Qt.WindowMinimizeButtonHint |
Qt.WindowMaximizeButtonHint |
Qt.WindowCloseButtonHint)
self.project = None
self.current_plugin = None
self.project_manager = ProjectManager(self)
self.plugins = self.load_plugins()
self.sidebar = Sidebar()
self.setup_ui()
self.setup_signals()
self.enable(False)
self.pipeline_model = PipelineModel()
self.sidebar.pl_list.setModel(self.pipeline_model)
self.pipeconf.pipeline_list.setModel(self.pipeline_model)
last = str(QSettings().value('path_of_last_project'))
if last:
quit_msg = "Load last project " + last + " ?"
reply = QMessageBox.question(self, 'Project Setup',
quit_msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
if last:
try:
self.open_project(last)
except:
qtutil.critical('Previous project appears to have been corrupted.\n \n'
+ traceback.format_exc(), self)
#qtutil.critical("Previous project appears to have been corrupted. Please move or delete it.")
self.sidebar.setup_sidebar_values(self.project)
def load_plugins(self):
"""This just gets all the plugins (no reference to pipeline)"""
plugins = collections.OrderedDict()
filenames = [f for f in sorted(os.listdir('plugins')) if f.endswith('.py')]
for filename in filenames:
name, ext = os.path.splitext(filename)
p = self.load_plugin('plugins.' + name, None)
if p:
plugins[name] = p
return plugins
def load_plugin(self, module, plugin_position):
try:
m = importlib.import_module(module)
if not hasattr(m, 'MyPlugin'):
return None
p = m.MyPlugin(self.project, plugin_position)
# p.run()
except:
print('Failed to import \'{}\'.'.format(module))
raise
else:
return p
# def reset_pipeline_plugins(self, plugin_names):
# for i, plugin_name in enumerate(plugin_names):
# p = self.load_plugin('plugins.' + plugin_name, i)
# if p:
# self.plugins[plugin_name] = p
# if self.current_plugin:
# self.set_plugin(self.current_plugin, None)
def reload_pipeline_plugins(self):
for i, plugin_name in enumerate(self.pipeline_model.get_plugin_names()):
p = self.load_plugin('plugins.' + plugin_name, i)
if p:
self.plugins[plugin_name] = p
# def set_x(val):
# self.sidebar.x_origin.setValue(val)
# def set_y(val):
# self.sidebar.y_origin.setValue(val)
# if plugin_name == 'set_coordinate_system':
# p.widget.x_origin_changed[float].connect(self.set_x)
# p.widget.y_origin_changed[float].connect(set_y)
if self.current_plugin:
self.set_plugin(self.current_plugin, None)
def setup_ui(self):
self.pipeconf = PipeconfDialog(self.plugins, self)
self.datadialog = DataDialog(self)
self.pl_frame = QFrame()
splitter = QSplitter(self)
self.enable = lambda yes: splitter.setEnabled(yes)
splitter.setHandleWidth(3)
splitter.setStyleSheet('QSplitter::handle {background: #cccccc;}')
splitter.addWidget(self.sidebar)
splitter.addWidget(self.pl_frame)
# splitter.setStretchFactor(0, 0)
# splitter.setStretchFactor(1, 1)
self.setCentralWidget(splitter)
self.menu = self.menuBar()
m = self.menu.addMenu('&File')
a = QAction('&New project', self)
a.setShortcut('Ctrl+N')
a.setStatusTip('Create new project')
a.triggered.connect(self.create_project)
m.addAction(a)
a = QAction('&Open project', self)
a.setShortcut('Ctrl+O')
a.setStatusTip('Open project')
a.triggered.connect(self.open_project)
m.addAction(a)
a = QAction("&Quit", self)
a.setShortcut("Ctrl+Q")
a.setStatusTip('Leave The App')
a.setIcon(QIcon('pics/quit.png'))
a.triggered.connect(self.close)
m.addAction(a)
about_action = QAction('&About ' + APPNAME, self)
about_action.setStatusTip('About ' + APPNAME)
about_action.triggered.connect(self.about)
about_action.setShortcut('F1')
whats_this_action = QWhatsThis.createAction(QAction('&What\'s This?', self))
whats_this_action.setShortcut('Shift+F1')
m = self.menu.addMenu('&Project')
m.setEnabled(False)
a = QAction("&Close", self)
a.setStatusTip('Close project')
a.triggered.connect(self.close_project)
m.addAction(a)
a = QAction("&Reset All Plugin Parameters", self)
a.setStatusTip('This is useful if you experience JSON-related issues allowing for a clean slate')
a.triggered.connect(self.reset_all_params)
m.addAction(a)
self.project_menu = m
help_menu = self.menu.addMenu('&Help')
help_menu.addAction(about_action)
help_menu.addAction(whats_this_action)
def reset_all_params(self):
for plugin_position, p in enumerate(self.project.pipeline):
if p['name'] in self.plugins.keys():
plugin = self.plugins[p['name']]
if hasattr(plugin, 'widget'):
if hasattr(plugin.widget, 'setup_params'):
if not hasattr(plugin.widget, 'params'):
plugin.widget.params = self.project.pipeline[plugin_position]
plugin.widget.project = self.project
plugin.widget.plugin_position = plugin_position
try:
plugin.widget.setup_params(reset=True)
except:
print("Failed to reset " + p['name'])
def setup_signals(self):
self.datadialog.reload_plugins.connect(self.reload_pipeline_plugins)
self.sidebar.open_pipeconf_requested.connect(self.open_pipeconf)
self.sidebar.open_datadialog_requested.connect(self.open_datadialog)
self.sidebar.automate_pipeline_requested.connect(self.automate_pipeline)
self.sidebar.x_origin_changed[float].connect(functools.partial(self.set_project_coordinate_system, 'x'))
self.sidebar.y_origin_changed[float].connect(functools.partial(self.set_project_coordinate_system, 'y'))
self.sidebar.units_per_pixel_changed[float].connect(functools.partial(self.set_project_coordinate_system,
'units_per_pixel'))
self.plugins['set_coordinate_system'].widget.x_origin_changed[float].connect(functools.partial(
self.set_project_coordinate_system, 'x'))
self.plugins['set_coordinate_system'].widget.y_origin_changed[float].connect(functools.partial(
self.set_project_coordinate_system, 'y'))
# todo: add signals from set_coordinate_system here
self.sidebar.pl_list.active_plugin_changed[str, int].connect(self.set_plugin)
self.sidebar.pl_list.setModel(self.pipeconf.pipeline_list.model())
def set_project_coordinate_system(self, key, value):
#todo: add update for view
self.project['origin'] = list(self.project['origin'])
if key == 'x':
self.project['origin'][0] = value
self.project.save()
elif key == 'y':
self.project['origin'][1] = value
self.project.save()
elif key == 'units_per_pixel':
self.project['unit_per_pixel'] = value
self.project.save()
if self.current_plugin in self.plugins.keys():
self.plugins[self.current_plugin].widget.view.update()
def create_project(self):
project = self.project_manager.new_project()
if project:
self.load_project(project)
def load_project(self, project):
self.clean()
self.project = project
self.setWindowTitle(APPNAME + ' - ' + project.name)
self.enable(True)
self.project_menu.setEnabled(True)
QSettings().setValue('path_of_last_project', project.path)
pipeline = []
for plugin_dict in self.project.pipeline:
# include fix to update old versions to new format
try:
plugin_name = plugin_dict['name']
except:
attrs = json.load(open('../templates/mbeproject.json'))
pipeline_template = attrs['pipeline']
# pipeline_names = [p['name'] for p in pipeline_template]
# plugins = self.load_plugins()
# for plugin_name in pipeline_names:
# for plugin in plugins:
# if plugin == plugin_name:
# pipeline.append((plugin, plugins[plugin].name))
# break
QMessageBox.about(self, 'Critical Error in pipeline. Manual Reset Recommended',
"""
<p>Please quit and replace the pipeline in your project JSON file with</p>
<p></p>
<td>%s</td>
<p>which can be copied from
<a href="https://github.com/Frikster/Mesoscale-Brain-Explorer/blob/master/templates/mbeproject.json">here</a></p>
<p>Only the pipeline section needs to be replaced</p>
""" % pipeline_template)
# qtutil.critical("Pipeline appears to be corrupt. "
# "Please replace your current pipeline in the JSON file with \n"
# " " + str(pipeline_template) + "which can be copied from \n" +
# < a href = "https://github.com/Frikster/Mesoscale-Brain-Explorer/issues" > here < / a > < / p >
# "https://github.com/Frikster/Mesoscale-Brain-Explorer/blob/master/templates/mbeproject.json")
return
for plugin in self.plugins:
if plugin == plugin_name:
pipeline.append((plugin, self.plugins[plugin].name))
break
self.pipeline_model.set_plugins(pipeline)
self.reload_pipeline_plugins()
self.sidebar.setup_sidebar_values(project)
# self.reset_pipeline_plugins([p[0] for p in pipeline])
def open_project(self, path=''):
project = self.project_manager.open_project(path)
if project:
self.load_project(project)
def close_project(self):
self.clean()
self.project = None
self.setWindowTitle(APPNAME)
self.project_menu.setEnabled(False)
self.enable(False)
def set_plugin(self, plugin_name, plugin_position):
p = self.load_plugin('plugins.' + str(plugin_name), plugin_position)
if not p:
return
self.current_plugin = plugin_name
self.plugins[plugin_name] = p
def set_x(val):
self.sidebar.x_origin.setValue(val)
def set_y(val):
self.sidebar.y_origin.setValue(val)
if plugin_name == 'set_coordinate_system':
p.widget.x_origin_changed[float].connect(set_x)
p.widget.y_origin_changed[float].connect(set_y)
lt = QVBoxLayout()
lt.addWidget(p.widget)
self.clean_plugin()
self.pl_frame.setLayout(lt)
# p.run()
def clean_plugin(self):
if self.pl_frame.layout():
clear_layout(self.pl_frame.layout())
QWidget().setLayout(self.pl_frame.layout())
def clean(self):
model = self.sidebar.pl_list.model()
if model:
model.clear()
self.clean_plugin()
def open_pipeconf(self):
self.pipeconf.exec_()
pipeline = self.pipeline_model.get_plugin_names()
self.project.set_pipeline(pipeline)
self.project.save()
def open_datadialog(self):
self.datadialog.update(self.project)
self.datadialog.exec_()
def automate_pipeline(self):
# order by index
ordered_q_model_indexes = sorted(self.sidebar.pl_list.selectedIndexes(), key=lambda x: x.row(), reverse=False)
if not ordered_q_model_indexes:
qtutil.info("Select all the plugins you want to process through. Use shift or ctrl to select multiple")
import_plugin_indexes = [ind for ind in range(len(ordered_q_model_indexes)) if
self.plugins[ordered_q_model_indexes[ind].data(Qt.UserRole)].name in
constants.IMPORT_PLUGINS]
if not import_plugin_indexes:
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected() # find the number of files outputted by the first plugin
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
if p.name not in constants.IMPORT_PLUGINS:
number_of_outputs = p.output_number_expected()
if not p.check_ready_for_automation(number_of_outputs):
qtutil.critical(p.automation_error_message())
return
number_of_outputs = p.output_number_expected(number_of_outputs) # find the number of outputs
p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
input_paths = p.get_input_paths()
if not input_paths:
qtutil.critical("The first plugin in the pipeline does not have a set of input files selected")
return
for q_model_index in ordered_q_model_indexes:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
ordered_q_model_indexes_segments = []
for i, import_ind in enumerate(import_plugin_indexes):
if i < len(import_plugin_indexes)-1:
# ordered_q_model_indexes are the indices in the GUI.
# retrieve the indices from where this import plugin is (import_ind) to
# the index right before the next import plugin
ordered_q_model_indexes_segment = ordered_q_model_indexes[import_ind:(import_plugin_indexes[i+1])]
else:
ordered_q_model_indexes_segment = ordered_q_model_indexes[import_ind:]
ordered_q_model_indexes_segments = ordered_q_model_indexes_segments + [ordered_q_model_indexes_segment]
import_paths = []
for i, ordered_q_model_indexes_segment in enumerate(ordered_q_model_indexes_segments):
import_plugin = self.plugins[ordered_q_model_indexes_segment[0].data(Qt.UserRole)]
qtutil.info("Please select all your files for the pipeline starting from import plugin " + str(i))
input_paths = import_plugin.get_input_paths()
import_paths = import_paths + [input_paths]
if not input_paths:
qtutil.critical("import plugin " + str(i) + " in the pipeline does not have a set of input files selected")
return
# ensure all selected plugins are ready for automation
for i, ordered_q_model_indexes_segment in enumerate(ordered_q_model_indexes_segments):
not_import_plugins = [self.plugins[ordered_q_model_indexes_segment[j].data(Qt.UserRole)] for j in
range(1, len(ordered_q_model_indexes_segment))]
number_of_outputs = len(import_paths[i])
for not_import_plugin in not_import_plugins:
if not not_import_plugin.check_ready_for_automation(number_of_outputs):
qtutil.critical(not_import_plugin.automation_error_message())
return
number_of_outputs = not_import_plugin.output_number_expected(number_of_outputs)
for i, ordered_q_model_indexes_segment in enumerate(ordered_q_model_indexes_segments):
input_paths = import_paths[i]
for q_model_index in ordered_q_model_indexes_segment:
p = self.plugins[q_model_index.data(Qt.UserRole)]
output_paths = p.run(input_paths)
input_paths = output_paths
# p = self.plugins[ordered_q_model_indexes[0].data(Qt.UserRole)]
# input_paths = p.get_input_paths()
# if not input_paths:
# qtutil.critical("The first plugin in the pipeline does not have a set of input files selected")
# return
#
# for q_model_index in ordered_q_model_indexes:
# p = self.plugins[q_model_index.data(Qt.UserRole)]
# output_paths = p.run(input_paths)
# input_paths = output_paths
# self.sidebar.pl_list.selectedIndexes()[0].data(Qt.UserRole)
#
# self.sidebar.pl_list.selectedIndexes()[0].row()
# self.sidebar.pl_list.model().data(self.sidebar.pl_list.selectedIndexes()[0])
def about(self):
author = 'Cornelis Dirk Haupt'
date = '2017'
QMessageBox.about(self, 'About ' + APPNAME,
"""
<b>%s</b>
<p>An online readme, including user manual and developer tutorial can be found
<a href="https://github.com/Frikster/Mesoscale-Brain-Explorer">here</a></p>
<p>Use the "what's this" feature to click on any UI component and learn how to use it</p>
<p>Please submit any feature requests or issues
<a href="https://github.com/Frikster/Mesoscale-Brain-Explorer/issues">here</a></p>
<p></p>
<p><table border="0" width="150">
<tr>
<td>Author:</td>
<td>%s</td>
</tr>
<tr>
<td>Version:</td>
<td>%s</td>
</tr>
<tr>
<td>Date:</td>
<td>%s</td>
</tr>
</table></p>
""" % (APPNAME, author, VERSION, date))
