def run(self, state):
if not self.unknowns and not state.unknowns:
if not self.configure():
state.canceled = True
return
review_req = []
unks = self.unknowns
for ai in unks:
ai.group_id = 0
if self.check_reviewed:
for attr in ('blanks', 'iso_evo'):
# check analyses to see if they have been reviewed
if attr not in review_req:
if not self.dvc.analysis_has_review(ai, attr):
review_req.append(attr)
if review_req:
information(
None, 'The current data set has been '
'analyzed and requires {}'.format(','.join(review_req)))
# add our analyses to the state
items = getattr(state, self.analysis_kind)
items.extend(self.unknowns)
state.projects = {ai.project for ai in state.unknowns}
def configure(self, pre_run=False, **kw):
if not pre_run:
self._manual_configured = True
if not self.path or not os.path.isfile(self.path):
msg = '''CSV File Format
Create/select a file with a column header as the first line.
The following columns are required:
runid, age, age_err
Optional columns are:
group, aliquot
e.x.
runid, age, age_error
SampleA, 10, 0.24
SampleB, 11, 0.32
SampleC, 10, 0.40'''
information(None, msg)
dlg = FileDialog()
if dlg.open() == OK:
self.path = dlg.path
return bool(self.path)
def _do_diff_fired(self):
if self.selected_commits:
lhs = self.selected_lhs
rhs = self.selected_rhs
lhsid = lhs.hexsha[:8]
lhsdate = isoformat_date(lhs.date)
rhsid = rhs.hexsha[:8]
rhsdate = rhs.date.isoformat()
diffs = []
for a in ('blanks', 'icfactors', 'intercepts'):
p = analysis_path((self.uuid, self.record_id),
self.repository_identifier,
modifier=a)
dd = get_diff(self.repo, lhs.hexsha, rhs.hexsha, p)
if dd:
diffs.append((a, dd))
if diffs:
v = DiffView(self.record_id, lhsid, rhsid, lhsdate, rhsdate)
for a, (aa, bb) in diffs:
func = getattr(v, 'set_{}'.format(a))
a = aa.data_stream.read().decode('utf-8')
b = bb.data_stream.read().decode('utf-8')
func(json.loads(a), json.loads(b))
v.finish()
open_view(v)
else:
information(
None,
'No Differences between {} and {}'.format(lhsid, rhsid))
def perform(self, event):
name = 'CurrentExperiment.txt'
path = os.path.join(paths.experiment_dir, name)
if not os.path.isfile(path):
information(None, 'No experiment called {}'.format(name))
open_experiment(event, path)
def _do_diff_fired(self):
if self.selected_commits:
lhs = self.selected_lhs
rhs = self.selected_rhs
lhsid = lhs.hexsha[:8]
lhsdate = isoformat_date(lhs.date)
rhsid = rhs.hexsha[:8]
rhsdate = rhs.date.isoformat()
diffs = []
for a in ('blanks', 'icfactors', 'intercepts'):
p = analysis_path((self.uuid, self.record_id), self.repository_identifier, modifier=a)
dd = get_diff(self.repo, lhs.hexsha, rhs.hexsha, p)
if dd:
diffs.append((a, dd))
if diffs:
v = DiffView(self.record_id, lhsid, rhsid, lhsdate, rhsdate)
for a, (aa, bb) in diffs:
func = getattr(v, 'set_{}'.format(a))
a = aa.data_stream.read().decode('utf-8')
b = bb.data_stream.read().decode('utf-8')
func(json.loads(a), json.loads(b))
v.finish()
open_view(v)
else:
information(None, 'No Differences between {} and {}'.format(lhsid, rhsid))
def perform(self, event):
name = 'CurrentExperiment.txt'
path = os.path.join(paths.experiment_dir, name)
if not os.path.isfile(path):
information(None, 'No experiment called {}'.format(name))
open_experiment(event, path)
def _open_via_finder_button_fired(self):
msg = '''CSV File Format
# Create/select a file with a column header as the first line.
# The following columns are required:
#
# runid, age, age_err
#
# Optional columns are:
#
# group, aliquot, sample
#
# e.x.
# runid, age, age_error
# Run1, 10, 0.24
# Run2, 11, 0.32
# Run3, 10, 0.40'''
information(None, msg)
dlg = FileDialog(default_directory=paths.csv_data_dir, action='open')
path = ''
if dlg.open() == OK:
if dlg.path:
path = dlg.path
self.in_path = path
def run(self, state):
if not self.unknowns and not state.unknowns:
if not self.configure():
state.canceled = True
return
review_req = []
unks = self.unknowns
for ai in unks:
ai.group_id = 0
if self.check_reviewed:
for attr in ('blanks', 'iso_evo'):
# check analyses to see if they have been reviewed
if attr not in review_req:
if not self.dvc.analysis_has_review(ai, attr):
review_req.append(attr)
if review_req:
information(None, 'The current data set has been '
'analyzed and requires {}'.format(','.join(review_req)))
# add our analyses to the state
items = getattr(state, self.analysis_kind)
items.extend(self.unknowns)
state.projects = {ai.project for ai in state.unknowns}
def close(self, info, is_ok):
print('asdf', info.object, info.object.commit_message)
if is_ok and not info.object.commit_message:
information(None, 'Please enter a commit message')
return False
return True
def perform(self, event):
from pychron.paths import paths
p = paths.hidden_path('analysis_sets')
if os.path.isfile(p):
if confirm(None, 'Are you sure you want to clear the Analysis Sets?') == YES:
os.remove(p)
else:
information(None, 'No Analysis Sets to remove')
def close(self, info, is_ok):
print('asdf', info.object, info.object.commit_message)
if is_ok and not info.object.commit_message:
information(None, 'Please enter a commit message')
return False
return True
def perform(self, event):
from pychron.paths import paths
p = paths.hidden_path('analysis_sets')
if os.path.isfile(p):
if confirm(None, 'Are you sure you want to clear the Analysis Sets?') == YES:
os.remove(p)
else:
information(None, 'No Analysis Sets to remove')
def _apply_history_button_fired(self):
if self.spectrometer:
self.spectrometer.set_gains(gains=self.selected.gains,
history=self.selected)
db = self.db
hist = db.get_gain_history(self.selected.hashkey)
hist.applied_date = datetime.now()
db.commit()
information(None, 'Gains update to {}'.format(self.selected.create_date))
def perform(self, event):
"""
goto issues page add an request or report bug
"""
app = event.task.window.application
name = app.preferences.get('pychron.general.remote')
if not name:
information(event.task.window.control, 'Please set an "Laboratory Repo" in General Preferences')
return
url = 'https://github.com/{}/issues/new'.format(name)
self._open_url(url)
def perform(self, event):
"""
goto issues page add an request or report bug
"""
app = event.task.window.application
name = app.preferences.get('pychron.general.remote')
if not name:
information(event.task.window.control, 'Please set an "Laboratory Repo" in General Preferences')
return
url = 'https://github.com/{}/issues/new'.format(name)
self._open_url(url)
def edit_key_bindings():
from pychron.core.ui.qt.keybinding_editor import KeyBindingsEditor
ks = [mKeyBinding(id=k,
binding=v[0],
description=v[1]) for k, v in user_key_map.items()]
kb = mKeyBindings(bindings=ks)
# kb.handle()
ed = KeyBindingsEditor(model=kb)
info = ed.edit_traits()
if info.result:
dump_key_bindings(kb.dump())
information(None, 'Changes take effect on Restart')
def edit_key_bindings():
from pychron.core.ui.qt.keybinding_editor import KeyBindingsEditor
ks = [mKeyBinding(id=k,
binding=v[0],
description=v[1]) for k, v in user_key_map.items()]
kb = mKeyBindings(bindings=ks)
# kb.handle()
ed = KeyBindingsEditor(model=kb)
info = ed.edit_traits()
if info.result:
dump_key_bindings(kb.dump())
information(None, 'Changes take effect on Restart')
def perform(self, event):
information(None, 'Upload to Geochron is not fully implemented')
app = event.task.application
geochron_service = app.get_service('pychron.geochron.geochron_service.GeochronService')
dvc = app.get_service(DVC_PROTOCOL)
with dvc.session_ctx():
ai = dvc.get_analysis('c038c72a-cf21-49f9-a5b5-1e43bb4a6b93')
ans = dvc.make_analyses(ai)
ag = AnalysisGroup()
ag.analyses = ans
print(geochron_service.assemble_xml(ag))
def _apply_button_fired(self):
gains = self.spectrometer.set_gains()
if gains:
db = self.db
hashkey = db.make_gains_hash(gains)
hist = db.get_gain_history(hashkey)
if not hist:
hist = db.add_gain_history(hashkey, save_type='manual')
for d, v in gains.items():
db.add_gain(d, v, hist)
hist.applied_date = datetime.now()
db.commit()
gainstr = '\n'.join(['{} {}'.format(*g) for g in gains.items()])
information(None, 'Gains set\n\n{}'.format(gainstr))
def perform(self, event):
information(None, 'Upload to Geochron is not fully implemented')
app = event.task.application
geochron_service = app.get_service(
'pychron.geochron.geochron_service.GeochronService')
dvc = app.get_service(DVC_PROTOCOL)
with dvc.session_ctx():
ai = dvc.get_analysis('c038c72a-cf21-49f9-a5b5-1e43bb4a6b93')
ans = dvc.make_analyses(ai)
ag = AnalysisGroup()
ag.analyses = ans
print(geochron_service.assemble_xml(ag))
def _click_to_show_instructions_fired(self):
m = information(None,
"\nTo remove spikes from the data:\n\n"
" 1. Click \"Show derivative histogram\" to "
"determine at what magnitude the spikes are present.\n"
" 2. Enter a suitable threshold (lower than the "
"lowest magnitude outlier in the histogram) in the "
"\"Threshold\" box, which will be the magnitude "
"from which to search. \n"
" 3. Click \"Find next\" to find the first spike.\n"
" 4. If desired, the width and position of the "
"boundaries used to replace the spike can be "
"adjusted by clicking and dragging on the displayed "
"plot.\n "
" 5. View the spike (and the replacement data that "
"will be added) and click \"Remove spike\" in order "
"to alter the data as shown. The tool will "
"automatically find the next spike to replace.\n"
" 6. Repeat this process for each spike throughout "
"the dataset, until the end of the dataset is "
"reached.\n"
" 7. Click \"OK\" when finished to close the spikes "
"removal tool.\n\n"
"Note: Various settings can be configured in "
"the \"Advanced settings\" section. Hover the "
"mouse over each parameter for a description of what "
"it does."
"\n",
title="Instructions"),
def _click_to_show_instructions_fired(self):
m = information(None, "\nTo remove spikes from the data:\n\n"
" 1. Click \"Show derivative histogram\" to "
"determine at what magnitude the spikes are present.\n"
" 2. Enter a suitable threshold (lower than the "
"lowest magnitude outlier in the histogram) in the "
"\"Threshold\" box, which will be the magnitude "
"from which to search. \n"
" 3. Click \"Find next\" to find the first spike.\n"
" 4. If desired, the width and position of the "
"boundaries used to replace the spike can be "
"adjusted by clicking and dragging on the displayed "
"plot.\n "
" 5. View the spike (and the replacement data that "
"will be added) and click \"Remove spike\" in order "
"to alter the data as shown. The tool will "
"automatically find the next spike to replace.\n"
" 6. Repeat this process for each spike throughout "
"the dataset, until the end of the dataset is "
"reached.\n"
" 7. Click \"OK\" when finished to close the spikes "
"removal tool.\n\n"
"Note: Various settings can be configured in "
"the \"Advanced settings\" section. Hover the "
"mouse over each parameter for a description of what "
"it does."
"\n",
title="Instructions"),
def set_interpreted_age(dvc, ias):
repos = dvc.get_local_repositories()
liths, groups, classes, types = get_lithology_values()
for ia in ias:
ia.lithology_classes = classes
ia.lithology_groups = groups
ia.lithology_types = types
ia.lithologies = liths
model = InterpretedAgeFactoryModel(items=ias, selected=ias[:1], dvc=dvc)
iaf = InterpretedAgeFactoryView(model=model, repository_identifiers=repos)
while 1:
info = iaf.edit_traits()
if info.result:
no_lat_lon = []
ias = [ia for ia in ias if ia.use]
for ia in ias:
if not ia.latitude and not ia.longitude:
no_lat_lon.append('{} ({})'.format(ia.name, ia.identifier))
if no_lat_lon:
n = ','.join(no_lat_lon)
if not confirm(
None,
'No Lat/Lon. entered for {}. Are you sure you want to continue without setting a '
'Lat/Lon?'.format(n)) == YES:
continue
ris = []
for rid, iass in groupby_key(ias, key='repository_identifier'):
if dvc.add_interpreted_ages(rid, iass):
ris.append(rid)
if ris:
if confirm(
None, 'Would you like to share changes to {}?'.format(
','.join(ris))) == YES:
for rid in ris:
dvc.push_repository(rid)
information(None, 'Sharing changes complete')
break
else:
break
def initialize_version(appname, debug):
root = os.path.dirname(__file__)
if not debug:
add_eggs(root)
else:
build_sys_path()
# can now use pychron.
from pychron.envisage.user_login import get_user
user = get_user()
if not user:
logger.info('user login failed')
return
if appname.startswith('py'):
appname = appname[2:]
from pychron.paths import paths
pref_path = os.path.join(paths.base, '.enthought',
'pychron.{}.application.{}'.format(appname, user),
'preferences.ini')
from ConfigParser import ConfigParser
cp = ConfigParser()
cp.read(pref_path)
proot = None
try:
proot = cp.get('pychron.general', 'root_dir')
except BaseException, e:
print 'root_dir exception={}'.format(e)
from pyface.directory_dialog import DirectoryDialog
information(
None,
'Pychron root directory not set in Preferences/General. Please select a valid directory'
)
dlg = DirectoryDialog(action='open',
default_directory=os.path.expanduser('~'))
result = dlg.open()
if result == OK:
proot = str(dlg.path)
def get_user(current=None):
"""
current: str, current user. if supplied omit from available list
"""
if os.path.isfile(login_file):
with open(login_file, 'r') as rfile:
u = rfile.read()
os.remove(login_file)
return u
users, last_login, isfile = load_user_file()
use_login, multi_user = get_last_login(last_login)
if use_login:
# check to see if the login file is set
# read the existing user file
if not isfile and multi_user:
information(None,
'Auto login as root. Quit to populate the user list')
dump_user_file(['root'], 'root')
return 'root'
if current:
users = [u for u in users if u != current]
login = Login(users=users)
if users:
login.user = last_login if last_login in users else users[0]
while 1:
info = login.edit_traits()
if info.result:
if login.user:
# add the manually entered user name to the users file
if not current and not multi_user:
if login.user not in users:
users.append(login.user)
dump_user_file(users, login.user)
return login.user
else:
break
else:
return 'root'
def get_user(current=None):
"""
current: str, current user. if supplied omit from available list
"""
if os.path.isfile(paths.login_file):
with open(paths.login_file, 'r') as fp:
u = fp.read()
os.remove(paths.login_file)
return u
users, last_login, isfile = load_user_file()
use_login, multi_user = get_last_login(last_login)
# print last_login, use_login
if use_login:
#check to see if the login file is set
#read the existing user file
if not isfile and multi_user:
information(None, 'Auto login as root. Quit to populate the user list')
dump_user_file(['root'], 'root')
return 'root'
if current:
users = [u for u in users if u != current]
login = Login(users=users)
if users:
login.user = last_login if last_login in users else users[0]
while 1:
info = login.edit_traits()
if info.result:
if login.user:
#add the manually entered user name to the users file
if not current and not multi_user:
if login.user not in users:
users.append(login.user)
dump_user_file(users, login.user)
return login.user
else:
break
else:
return 'root'
def perform(self, event):
import os
from pychron.globals import globalv
from pychron.paths import paths
name = self.fname
if globalv.debug:
p = os.path.join(paths.data_dir, '{}_template.txt'.format(name.lower()))
else:
p = None
dlg = FileDialog(action='save as', default_directory=paths.data_dir)
if dlg.open():
p = dlg.path
if p is not None:
with open(p, 'w') as wfile:
wfile.write(self.template)
information(event.task.window.control, 'An example {} template was written to {}\n\n'
'Replace the placeholder data in the file with your data\n'
'Make sure to use "TABS" to deliminate columns'.format(name, p))
def initialize_version(appname, debug):
root = os.path.dirname(__file__)
if not debug:
add_eggs(root)
else:
build_sys_path()
# can now use pychron.
from pychron.envisage.user_login import get_user
user = get_user()
if not user:
logger.info("user login failed")
return
if appname.startswith("py"):
appname = appname[2:]
from pychron.paths import paths
pref_path = os.path.join(
paths.base, ".enthought", "pychron.{}.application.{}".format(appname, user), "preferences.ini"
)
from ConfigParser import ConfigParser
cp = ConfigParser()
cp.read(pref_path)
proot = None
try:
proot = cp.get("pychron.general", "root_dir")
except BaseException, e:
print "root_dir exception={}".format(e)
from pyface.directory_dialog import DirectoryDialog
information(None, "Pychron root directory not set in Preferences/General. Please select a valid directory")
dlg = DirectoryDialog(action="open", default_directory=os.path.expanduser("~"))
result = dlg.open()
if result == OK:
proot = str(dlg.path)
def perform(self, event):
from git import Repo
from git.exc import InvalidGitRepositoryError
from pychron.paths import paths
remote = 'origin'
branch = 'master'
repos = []
for d in os.listdir(paths.repository_dataset_dir):
if d.startswith('.') or d.startswith('~'):
continue
try:
r = Repo(repository_path(d))
except InvalidGitRepositoryError:
continue
repos.append(r)
n = len(repos)
pd = myProgressDialog(max=n - 1, can_cancel=True, can_ok=False)
pd.open()
shared = False
for r in repos:
pd.change_message('Fetch {}'.format(os.path.basename(
r.working_dir)))
c = r.git.log('{}/{}..HEAD'.format(remote, branch), '--oneline')
if c:
r.git.pull()
d = os.path.basename(r.working_dir)
if confirm(None,
'Share changes made to {}.\n\n{}'.format(d,
c)) == YES:
r.git.push(remote, branch)
shared = True
msg = 'Changes successfully shared' if shared else 'No changes to share'
information(None, msg)
def perform(self, event):
from git import Repo
from git.exc import InvalidGitRepositoryError
from pychron.paths import paths
remote = 'origin'
branch = 'master'
repos = []
for d in os.listdir(paths.repository_dataset_dir):
if d.startswith('.') or d.startswith('~'):
continue
try:
r = Repo(repository_path(d))
except InvalidGitRepositoryError:
continue
repos.append(r)
n = len(repos)
pd = myProgressDialog(max=n - 1,
can_cancel=True,
can_ok=False)
pd.open()
shared = False
for r in repos:
pd.change_message('Fetch {}'.format(os.path.basename(r.working_dir)))
c = r.git.log('{}/{}..HEAD'.format(remote, branch), '--oneline')
if c:
r.git.pull()
d = os.path.basename(r.working_dir)
if confirm(None, 'Share changes made to {}.\n\n{}'.format(d, c)) == YES:
r.git.push(remote, branch)
shared = True
msg = 'Changes successfully shared' if shared else 'No changes to share'
information(None, msg)
def perform(self, event):
app = event.task.window.application
name = app.preferences.get('pychron.general.remote')
if not name:
information(
event.task.window.control,
'Please set an "Laboratory Repo" in General Preferences')
return
from pychron.envisage.settings_repo import SettingsRepoManager
from pychron.paths import paths
root = os.path.join(paths.root_dir, '.lab')
exists = os.path.isdir(os.path.join(root, '.git'))
if exists:
repo = SettingsRepoManager()
repo.path = root
repo.open_repo(root)
repo.pull()
else:
url = 'https://github.com/{}'.format(name)
repo = SettingsRepoManager.clone_from(url, root)
self._perform(repo)
def perform(self, event):
from pychron.dvc.work_offline import switch_to_offline_database
app = event.task.window.application
switch_to_offline_database(app.preferences)
information(None, 'You are now using the offline database. Close any Browser or Pipeline windows to activate '
'offline database')
def _click_to_show_instructions_fired(self):
from pyface.message_dialog import information
m = information(None, SPIKES_REMOVAL_INSTRUCTIONS,
title="Instructions"),
def _do_diff_fired(self):
if self.selected_commits:
# n = len(self.selected_commits)
# lhs = self.selected_lhs
# if n == 1:
# rhsid = 'HEAD'
# obj = self.repo.head.commit
# rhsdate = isoformat_date(obj.committed_date)
# if lhs.tag == 'IMPORT':
# diffs = []
# for a in ('blanks', 'icfactors', 'tags', 'intercepts'):
# p = analysis_path(self.record_id, self.repository_identifier, modifier=a)
# dd = get_diff(self.repo, lhs.hexsha, 'HEAD', p)
# if dd:
# diffs.append((a, dd))
# if diffs:
# v = ImportDiffView(self.record_id, lhsid, rhsid, lhsdate, rhsdate)
# for a, (aa, bb) in diffs:
# func = getattr(v, 'set_{}'.format(a))
# func(json.load(aa.data_stream),
# json.load(bb.data_stream))
# v.finish()
# open_view(v)
#
# return
# else:
# d = get_diff(self.repo, lhs.hexsha, 'HEAD', lhs.path)
#
# elif n == 2:
# lhs = self.selected_lhs
# rhs = self.selected_rhs
# else:
# warning(None, 'Can only diff max of 2')
# return
lhs = self.selected_lhs
rhs = self.selected_rhs
lhsid = lhs.hexsha[:8]
lhsdate = isoformat_date(lhs.date)
rhsid = rhs.hexsha[:8]
rhsdate = rhs.date.isoformat()
diffs = []
for a in ('blanks', 'icfactors', 'tags', 'intercepts'):
p = analysis_path(self.record_id, self.repository_identifier, modifier=a)
dd = get_diff(self.repo, lhs.hexsha, rhs.hexsha, p)
if dd:
diffs.append((a, dd))
if diffs:
v = DiffView(self.record_id, lhsid, rhsid, lhsdate, rhsdate)
for a, (aa, bb) in diffs:
func = getattr(v, 'set_{}'.format(a))
func(json.load(aa.data_stream),
json.load(bb.data_stream))
v.finish()
open_view(v)
else:
information(None, 'No Differences between {} and {}'.format(lhsid, rhsid))
def show_evolutions_factory(record_id,
isotopes,
show_evo=True,
show_equilibration=False,
show_baseline=False):
if WINDOW_CNT > 20:
information(
None,
'You have too many Isotope Evolution windows open. Close some before proceeding'
)
return
from pychron.graph.stacked_regression_graph import StackedRegressionGraph
if not show_evo:
xmi = Inf
xma = -Inf
else:
xmi, xma = 0, -Inf
g = StackedRegressionGraph(resizable=True)
g.plotcontainer.spacing = 10
g.window_height = min(275 * len(isotopes), 800)
g.window_x = OX + XOFFSET * WINDOW_CNT
g.window_y = OY + YOFFSET * WINDOW_CNT
isotopes = sort_isotopes(isotopes, reverse=False, key=lambda x: x.name)
for i, iso in enumerate(isotopes):
ymi, yma = Inf, -Inf
p = g.new_plot(padding=[80, 10, 10, 40])
g.add_limit_tool(p, 'x')
g.add_limit_tool(p, 'y')
g.add_axis_tool(p, p.x_axis)
g.add_axis_tool(p, p.y_axis)
p.y_axis.title_spacing = 50
if show_equilibration:
sniff = iso.sniff
g.new_series(sniff.xs,
sniff.ys,
type='scatter',
fit=None,
color='red')
ymi, yma = min_max(ymi, yma, sniff.ys)
xmi, xma = min_max(xmi, xma, sniff.xs)
if show_evo:
g.new_series(iso.xs,
iso.ys,
fit=iso.fit,
filter_outliers_dict=iso.filter_outliers_dict,
color='black')
ymi, yma = min_max(ymi, yma, iso.ys)
xmi, xma = min_max(xmi, xma, iso.xs)
if show_baseline:
baseline = iso.baseline
g.new_series(baseline.xs,
baseline.ys,
type='scatter',
fit=baseline.fit,
filter_outliers_dict=baseline.filter_outliers_dict,
color='blue')
ymi, yma = min_max(ymi, yma, baseline.ys)
xmi, xma = min_max(xmi, xma, baseline.xs)
g.set_x_limits(min_=xmi, max_=xma, pad='0.025,0.05')
g.set_y_limits(min_=ymi, max_=yma, pad='0.05', plotid=i)
g.set_x_title('Time (s)', plotid=i)
g.set_y_title('{} (fA)'.format(iso.name), plotid=i)
g.refresh()
g.window_title = '{} {}'.format(
record_id, ','.join([i.name for i in reversed(isotopes)]))
return g
def information_dialog(self, msg, title=None):
if title is None:
information(None, msg)
else:
information(None, msg, title=title)
def show_evolutions_factory(record_id, isotopes, show_evo=True, show_equilibration=False, show_baseline=False):
if WINDOW_CNT > 20:
information(None, 'You have too many Isotope Evolution windows open. Close some before proceeding')
return
from pychron.graph.stacked_regression_graph import StackedRegressionGraph
if not show_evo:
xmi = Inf
xma = -Inf
else:
xmi, xma = 0, -Inf
g = StackedRegressionGraph(resizable=True)
g.plotcontainer.spacing = 10
g.window_height = min(275 * len(isotopes), 800)
g.window_x = OX + XOFFSET * WINDOW_CNT
g.window_y = OY + YOFFSET * WINDOW_CNT
isotopes = sort_isotopes(isotopes, reverse=False, key=lambda x: x.name)
for i, iso in enumerate(isotopes):
ymi, yma = Inf, -Inf
p = g.new_plot(padding=[80, 10, 10, 40])
g.add_limit_tool(p, 'x')
g.add_limit_tool(p, 'y')
g.add_axis_tool(p, p.x_axis)
g.add_axis_tool(p, p.y_axis)
p.y_axis.title_spacing = 50
if show_equilibration:
sniff = iso.sniff
g.new_series(sniff.xs, sniff.ys,
type='scatter',
fit=None,
color='red')
ymi, yma = min_max(ymi, yma, sniff.ys)
xmi, xma = min_max(xmi, xma, sniff.xs)
if show_evo:
g.new_series(iso.xs, iso.ys,
fit=iso.fit,
filter_outliers_dict=iso.filter_outliers_dict,
color='black')
ymi, yma = min_max(ymi, yma, iso.ys)
xmi, xma = min_max(xmi, xma, iso.xs)
if show_baseline:
baseline = iso.baseline
g.new_series(baseline.xs, baseline.ys,
type='scatter', fit=baseline.fit,
filter_outliers_dict=baseline.filter_outliers_dict,
color='blue')
ymi, yma = min_max(ymi, yma, baseline.ys)
xmi, xma = min_max(xmi, xma, baseline.xs)
g.set_x_limits(min_=xmi, max_=xma, pad='0.025,0.05')
g.set_y_limits(min_=ymi, max_=yma, pad='0.05', plotid=i)
g.set_x_title('Time (s)', plotid=i)
g.set_y_title('{} (fA)'.format(iso.name), plotid=i)
g.refresh()
g.window_title = '{} {}'.format(record_id, ','.join([i.name for i in reversed(isotopes)]))
return g
def _do_diff_fired(self):
if self.selected_commits:
# n = len(self.selected_commits)
# lhs = self.selected_lhs
# if n == 1:
# rhsid = 'HEAD'
# obj = self.repo.head.commit
# rhsdate = isoformat_date(obj.committed_date)
# if lhs.tag == 'IMPORT':
# diffs = []
# for a in ('blanks', 'icfactors', 'tags', 'intercepts'):
# p = analysis_path(self.record_id, self.repository_identifier, modifier=a)
# dd = get_diff(self.repo, lhs.hexsha, 'HEAD', p)
# if dd:
# diffs.append((a, dd))
# if diffs:
# v = ImportDiffView(self.record_id, lhsid, rhsid, lhsdate, rhsdate)
# for a, (aa, bb) in diffs:
# func = getattr(v, 'set_{}'.format(a))
# func(json.load(aa.data_stream),
# json.load(bb.data_stream))
# v.finish()
# open_view(v)
#
# return
# else:
# d = get_diff(self.repo, lhs.hexsha, 'HEAD', lhs.path)
#
# elif n == 2:
# lhs = self.selected_lhs
# rhs = self.selected_rhs
# else:
# warning(None, 'Can only diff max of 2')
# return
lhs = self.selected_lhs
rhs = self.selected_rhs
lhsid = lhs.hexsha[:8]
lhsdate = isoformat_date(lhs.date)
rhsid = rhs.hexsha[:8]
rhsdate = rhs.date.isoformat()
diffs = []
for a in ('blanks', 'icfactors', 'tags', 'intercepts'):
p = analysis_path(self.record_id,
self.repository_identifier,
modifier=a)
dd = get_diff(self.repo, lhs.hexsha, rhs.hexsha, p)
if dd:
diffs.append((a, dd))
if diffs:
v = DiffView(self.record_id, lhsid, rhsid, lhsdate, rhsdate)
for a, (aa, bb) in diffs:
func = getattr(v, 'set_{}'.format(a))
func(json.load(aa.data_stream), json.load(bb.data_stream))
v.finish()
open_view(v)
else:
information(
None,
'No Differences between {} and {}'.format(lhsid, rhsid))
def show_evolutions_factory(record_id,
isotopes,
show_evo=True,
show_equilibration=False,
show_baseline=False,
show_statistics=False,
ncols=1,
scale_to_equilibration=False):
if WINDOW_CNT > 20:
information(
None,
'You have too many Isotope Evolution windows open. Close some before proceeding'
)
return
if not show_evo:
xmi = Inf
xma = -Inf
else:
xmi, xma = 0, -Inf
if ncols > 1:
isotopes = sort_isotopes(isotopes,
reverse=True,
key=attrgetter('name'))
def reorder(l, n):
l = [l[i:i + n] for i in range(0, len(l), n)]
nl = []
for ri in range(len(l[0])):
for col in l:
try:
nl.append(col[ri])
except IndexError:
pass
return nl
nrows = ceil(len(isotopes) / ncols)
isotopes = reorder(isotopes, nrows)
g = ColumnStackedRegressionGraph(resizable=True,
ncols=ncols,
nrows=nrows,
container_dict={
'padding_top': 15 * nrows,
'spacing': (0, 15),
'padding_bottom': 40
})
resizable = 'hv'
else:
resizable = 'h'
isotopes = sort_isotopes(isotopes,
reverse=False,
key=attrgetter('name'))
g = StackedRegressionGraph(resizable=True,
container_dict={'spacing': 15})
# g.plotcontainer.spacing = 10
g.window_height = min(275 * len(isotopes), 800)
g.window_x = OX + XOFFSET * WINDOW_CNT
g.window_y = OY + YOFFSET * WINDOW_CNT
for i, iso in enumerate(isotopes):
ymi, yma = Inf, -Inf
p = g.new_plot(padding=[80, 10, 10, 40], resizable=resizable)
g.add_limit_tool(p, 'x')
g.add_limit_tool(p, 'y')
g.add_axis_tool(p, p.x_axis)
g.add_axis_tool(p, p.y_axis)
if show_statistics:
g.add_statistics(i)
p.y_axis.title_spacing = 50
if show_equilibration:
sniff = iso.sniff
if sniff.xs.shape[0]:
g.new_series(sniff.offset_xs,
sniff.ys,
type='scatter',
fit=None,
color='red')
ymi, yma = min_max(ymi, yma, sniff.ys)
xmi, xma = min_max(xmi, xma, sniff.offset_xs)
if show_evo:
if iso.fit is None:
iso.fit = 'linear'
g.new_series(iso.offset_xs,
iso.ys,
fit=iso.efit,
truncate=iso.truncate,
filter_outliers_dict=iso.filter_outliers_dict,
color='black')
g.set_regressor(iso.regressor, i)
xmi, xma = min_max(xmi, xma, iso.offset_xs)
if not scale_to_equilibration:
ymi, yma = min_max(ymi, yma, iso.ys)
if show_baseline:
baseline = iso.baseline
g.new_series(baseline.offset_xs,
baseline.ys,
type='scatter',
fit=baseline.efit,
filter_outliers_dict=baseline.filter_outliers_dict,
color='blue')
xmi, xma = min_max(xmi, xma, baseline.offset_xs)
if not scale_to_equilibration:
ymi, yma = min_max(ymi, yma, baseline.ys)
xpad = '0.025,0.05'
ypad = '0.05'
if scale_to_equilibration:
ypad = None
r = (yma - ymi) * 0.02
# ymi = yma - r
fit = iso.fit
if fit != 'average':
fit, _ = convert_fit(iso.fit)
fy = polyval(polyfit(iso.offset_xs, iso.ys, fit), 0)
if ymi > fy:
ymi = fy - r
fy = polyval(polyfit(iso.offset_xs, iso.ys, fit), xma)
if fy > yma:
yma = fy
elif fy < ymi:
ymi = fy - r
# yma += r
g.set_x_limits(min_=xmi, max_=xma, pad=xpad)
g.set_y_limits(min_=ymi, max_=yma, pad=ypad, plotid=i)
g.set_x_title('Time (s)', plotid=i)
g.set_y_title('{} ({})'.format(iso.name, iso.units), plotid=i)
g.refresh()
g.window_title = '{} {}'.format(
record_id, ','.join([i.name for i in reversed(isotopes)]))
return g
def import_db(self, info):
result, url = self.model.import_db()
if result:
information(None, 'Added to database.\n\n {}'.format(url))
else:
warning(None, 'Unable to connect to database.\n\n {}'.format(url))
def _sync_metadata_button_fired(self):
with self.dvc.session_ctx():
for it in self.items:
self.dvc.sync_ia_metadata(it)
information(None, 'Metadata sync complete')
def information(self, message, title='Information'):
""" Convenience method to show an information message dialog. """
from pyface.message_dialog import information
return information(self.window.control, message, title)
def information(self, message, title='Information'):
""" Convenience method to show an information message dialog. """
from pyface.message_dialog import information
return information(self.window.control, message, title)
