def on_save_workspace(self, evt):
if not self.confirm_properties():
return
p = Properties()
dlg = wx.FileDialog(
self,
message="Save workspace as...",
defaultDir=os.getcwd(),
defaultFile='%s_%s.workspace' % (os.path.splitext(
os.path.split(p._filename)[1])[0], p.image_table),
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT | wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
wx.GetApp().save_workspace(dlg.GetPath())
def on_save_properties(self, evt):
if not self.confirm_properties():
return
p = Properties()
dirname, filename = os.path.split(p._filename)
ext = os.path.splitext(p._filename)[-1]
dlg = wx.FileDialog(self,
message="Save properties as...",
defaultDir=dirname,
defaultFile=filename,
wildcard=ext,
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT
| wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
p.save_file(dlg.GetPath())
def Start(self):
'''Initialize CPA
'''
if hasattr(sys, "frozen") and sys.platform == "darwin":
# Some versions of Macos like to put CPA in a sandbox. If we're frozen Java should be packed in,
# so let's just figure out the directory on run time.
os.environ["CP_JAVA_HOME"] = os.path.abspath(
os.path.join(sys.prefix, "..", "Resources/Home"))
'''List of tables created by the user during this session'''
self.user_tables = []
p = Properties()
self.frame = MainGUI(p, None, size=(1000, -1))
self.frame.Show() # Show frame
if not p.is_initialized():
from cpa.guiutils import show_load_dialog
try:
if not show_load_dialog():
example_link_address = 'cellprofileranalyst.org'
dlg = wx.MessageDialog(
None,
'CellProfiler Analyst requires a properties file. Download an example at %s'
% (example_link_address), 'Properties file required',
wx.OK)
response = dlg.ShowModal()
logging.error(
'CellProfiler Analyst requires a properties file.')
return False
else:
db = DBConnect()
db.connect()
db.register_gui_parent(self.frame)
except Exception as e:
p._initialized = False
# Fully raising the exception during this startup sequence will crash CPA.
# So we'll display it manually.
show_exception_as_dialog(type(e),
e,
e.__traceback__,
raisefurther=False)
logging.critical(e)
try:
from cpa.updatechecker import check_update
check_update(self.frame, event=False)
except:
logging.warn("CPA was unable to check for updates.")
return True
def clear_link_tables(self, evt=None):
if not self.confirm_properties():
return
p = Properties()
dlg = wx.MessageDialog(
self, 'This will delete the tables '
'"%s" and "%s" from your database. '
'CPA will automatically recreate these tables as it '
'discovers how your database is linked. Are you sure you '
'want to proceed?' % (p.link_tables_table, p.link_columns_table),
'Clear table linking information?',
wx.YES_NO | wx.NO_DEFAULT | wx.ICON_QUESTION)
response = dlg.ShowModal()
if response != wx.ID_YES:
return
db = DBConnect()
db.execute('DROP TABLE IF EXISTS %s' % (p.link_tables_table))
db.execute('DROP TABLE IF EXISTS %s' % (p.link_columns_table))
db.Commit()
def on_load_properties(self, evt):
# Show confirmation dialog.
if self.properties.is_initialized():
dlg = wx.MessageDialog(
None,
"Loading a new file will close all windows and clear unsaved data. Proceed?",
'Load properties file', wx.OK | wx.CANCEL)
response = dlg.ShowModal()
if response != wx.ID_OK:
return
# Close all subwindows
for window in self.GetChildren():
if isinstance(window, wx.Frame):
window.Destroy()
# Shut down existing connections and wipe properties.
db = DBConnect()
db.Disconnect()
p = Properties()
p.clear()
self.console.Clear()
if not p.is_initialized():
from cpa.guiutils import show_load_dialog
if not show_load_dialog():
example_link_address = 'cellprofileranalyst.org'
dlg = wx.MessageDialog(
None,
'CellProfiler Analyst requires a properties file. Download an example at %s'
% (example_link_address), 'Properties file required',
wx.OK)
response = dlg.ShowModal()
logging.error(
'CellProfiler Analyst requires a properties file.')
else:
db.connect()
db.register_gui_parent(self)
import unittest
from cpa.imagereader import ImageReader
from cpa.properties import Properties
p = Properties()
# fake-up some props
p._filename = '../../CPAnalyst_test_data/test_images/'
p.image_channel_colors = ['red', 'green', 'blue', 'none', 'none', 'none']
p.object_name = ['cell', 'cells']
p.image_names = ['', '', '']
p.image_id = 'ImageNumber'
ir = ImageReader()
class TestImageReader(unittest.TestCase):
def test_tif1(self):
# TIF RGB, 8-bit, PackBits encoding
fds = ['color.tif']
images = ir.ReadImages(fds)
assert len(images) == 3
for im in images:
assert 0. <= im.min() <= im.max() <= 1.
assert im.shape == (512, 512)
def test_tif2(self):
# 2 RGB TIFS
fds = ['color.tif', 'color.tif']
images = ir.ReadImages(fds)
assert len(images) == 6
def setup_mysql(self):
self.p = Properties()
self.db = DBConnect()
self.db.Disconnect()
self.p.LoadFile('../../CPAnalyst_test_data/nirht_test.properties')
def setup_sqlite2(self):
self.p = Properties()
self.db = DBConnect()
self.db.Disconnect()
self.p.LoadFile(
'../../CPAnalyst_test_data/export_to_db_test.properties')
