def onButtonCheckPOIs(self, event):
dir0 = os.path.join(self.dir0, 'dbrr')
if not os.path.exists(dir0):
wx.MessageBox('Registration must be conducted and parameters applied before checking POIs.', 'Error:', wx.OK)
if not os.path.exists( os.path.join(self.dir0, '_poi.npy') ):
wx.MessageBox('POIs must be defined before checking.\nUse the "POI analysis" button to define POIs', 'Error:', wx.OK)
else:
self.metadata = DB.load_metadata(self.dir0)
POI = self.metadata.load_pois()
allnone = True
for poi in POI:
for p in poi:
if p!=None:
allnone = False
break
if allnone:
wx.MessageBox('Warning: No POIs defined.\nUse the "POI analysis" button to define POIs', 'Error:', wx.OK)
else:
dialog = ppp_selector.PPDatabaseQueryDialog(self.metadata, by_foot=True)
dialog.ShowModal()
subj = None
if not dialog.canceled:
canceled = dialog.canceled
if not canceled:
subj,byfoot,LR,FH,alltrials,trials = dialog.get_choices()
dialog.Destroy()
if subj!=None:
subjname = self.metadata.USUBJ[subj]
footlabel = self.metadata.get_foot_label(LR, FH)
frame = checkpoiGUI.CheckPOIFrame(None, -1, 'PPP Check POIs (%s: %s)'%(subjname,footlabel), metadata=self.metadata, subj=subj, LR=LR, FH=FH)
frame.Show(True)
def onButtonExportMeans(self, event):
dir0 = os.path.join(self.dir0, 'dbrr')
if not os.path.exists(dir0):
wx.MessageBox('Registration must be conducted and parameters applied before exporting COP trajectories.', 'Error:', wx.OK)
else:
result = wx.MessageBox('Computing means may take several minutes.\nPress OK to continue.', 'Note:', wx.OK|wx.CANCEL)
if result == wx.OK:
dir1 = os.path.join(self.dir0, 'dbmeans')
if not os.path.exists(dir1):
os.mkdir(dir1)
dialog = wx.ProgressDialog("", "Computing means and saving to ./dbmeans...", maximum=4*self.metadata.nSubj, style=wx.PD_ELAPSED_TIME)
self.metadata = DB.load_metadata(self.dir0)
ii = 0
for subj in range(self.metadata.nSubj):
i = 0
for FH in [False,True]:
for LR in [False,True]:
rollovers = self.metadata.get_rollovers(subj, LR=LR, FH=FH, only_good=True)
II = self.metadata.load_rollovers(rollovers, dbdir='dbrr', max=True)
II = np.dstack(II)
I = II.mean(axis=2)
fname1 = os.path.join(dir1, 'subj%03d_mean%d.h5'%(subj,i))
PM.save(fname1, I)
dialog.Update(ii)
i += 1
ii += 1
dialog.Destroy()
def onButtonCheckMeans(self, event):
dir0 = os.path.join(self.dir0, 'dbmeans')
if not os.path.exists(dir0):
wx.MessageBox('Means not yet computed.\nUse "Export means" from the main menu.', 'Error:', wx.OK)
else:
self.metadata = DB.load_metadata(self.dir0)
frame = checkmeansGUI.CheckMeansFrame(None, -1, 'PPP Check Means', metadata=self.metadata)
frame.Show(True)
def onButtonPOI(self, event):
if not os.path.exists( os.path.join(self.dir0, 'dbmeans') ):
wx.MessageBox('Mean images must be exported before conducting POI analysis.', 'Error:', wx.OK)
else:
self.metadata = DB.load_metadata(self.dir0)
if not os.path.exists( os.path.join(self.dir0, '_poi.npy') ):
self.metadata.save_pois()
frame = poiGUI.POIFrame(None, -1, 'PPP POI Selector', metadata=self.metadata)
frame.Show(True)
def OnInit(self): import pressure_database as DB; reload(DB) # dir0 = '/Volumes/DataProc/projectsExternal/uQueensland/test2/' dir0 = '/Users/todd/Desktop/test2' metadata = DB.load_metadata(dir0) subj = 0 frame = POIFrame(None, -1, 'Points of Interest (POIs)', metadata=metadata) frame.Show(True) self.SetTopWindow(frame) return True
def onButtonCheckFeet(self, event): metadata = DB.load_metadata(self.dir0) self.metadata = metadata dialog = ppp_selector.PPDatabaseQueryDialog(metadata, by_foot=True, only_good=True) dialog.ShowModal() rollovers = None if not dialog.canceled: rollovers = dialog.get_rollovers() dialog.Destroy() if rollovers!=None: frame = checkfeetGUI.CheckFeetFrame(None, -1, 'PPP Check Foot Labels', metadata=metadata, rollovers=rollovers) frame.Show(True)
def OnInit(self):
import pressure_database as DB
reload(DB)
# dir0 = '/Volumes/DataProc/projectsExternal/uQueensland/test2/'
dir0 = '/Users/todd/Desktop/test2'
metadata = DB.load_metadata(dir0)
subj = 0
frame = POIFrame(None,
-1,
'Points of Interest (POIs)',
metadata=metadata)
frame.Show(True)
self.SetTopWindow(frame)
return True
def onButtonIdentify(self, event):
if not os.path.exists( os.path.join(self.dir0, 'dbr') ):
result = wx.MessageBox('Images must be resized before idenitfying feet.\nSelect "Resize image grids" from the main menu.', 'Error.', wx.OK)
return
self.metadata = DB.load_metadata(self.dir0)
dialog = ppp_selector.PPDatabaseQueryDialog(self.metadata, by_trial=True)
dialog.ShowModal()
rollovers = None
if not dialog.canceled:
rollovers = dialog.get_rollovers(group_by_trial=True)
dialog.Destroy()
if rollovers!=None:
frame = identifyGUI.IdentifyFrame(None, -1, 'PPP Foot Identificaiton', metadata=self.metadata, rollovers=rollovers)
frame.Show(True)
def onButtonTemplates(self, event):
metadata = DB.load_metadata(self.dir0)
labels = ['Fore Left', 'Fore Right', 'Hind Left', 'Hind Right']
### check that good feet are available for all subjects:
for subj in range(metadata.nSubj):
n = metadata.get_nrollovers_by_subj(subj, only_good=True)
if np.any( np.array(n)<1 ):
ind = np.argwhere(np.array(n)<1).flatten()
ind = ind[0]
label = labels[ind]
result = wx.MessageBox('No good rollovers found for subject "%s", foot: "%s".\nYou must identify at least one good rollover to proceed.'%(metadata.USUBJ[subj], label), 'Error', wx.OK)
return None
self.metadata = metadata
frame = templateGUI.TemplateFrame(None, -1, 'PPP Template Selection', metadata=metadata)
frame.Show(True)
def onButtonRegister(self, event): self.metadata = DB.load_metadata(self.dir0) if not os.path.exists( os.path.join(self.dir0, '_registration_params.npy') ): self.metadata.save_registration_parameters() dialog = ppp_selector.PPDatabaseQueryDialog(self.metadata, by_foot=True) dialog.ShowModal() subj = None if not dialog.canceled: canceled = dialog.canceled if not canceled: subj,byfoot,LR,FH,alltrials,trials = dialog.get_choices() dialog.Destroy() if subj!=None: subjname = self.metadata.USUBJ[subj] footlabel = self.metadata.get_foot_label(LR, FH) frame = registrationGUI.RegistrationFrame(None, -1, 'PPP Registration (%s: %s)'%(subjname,footlabel), metadata=self.metadata, subj=subj, LR=LR, FH=FH) frame.Show(True)
def onButtonCheckRegistration(self, event):
dir0 = os.path.join(self.dir0, 'dbrr')
if not os.path.exists(dir0):
wx.MessageBox('Registration must be conducted and parameters applied before checking registration.', 'Error:', wx.OK)
else:
self.metadata = DB.load_metadata(self.dir0)
dialog = ppp_selector.PPDatabaseQueryDialog(self.metadata, by_foot=True)
dialog.ShowModal()
subj = None
if not dialog.canceled:
canceled = dialog.canceled
if not canceled:
subj,byfoot,LR,FH,alltrials,trials = dialog.get_choices()
dialog.Destroy()
if subj!=None:
subjname = self.metadata.USUBJ[subj]
footlabel = self.metadata.get_foot_label(LR, FH)
frame = checkregistrationGUI.CheckRegistrationFrame(None, -1, 'PPP Check Registration (%s: %s)'%(subjname,footlabel), metadata=self.metadata, subj=subj, LR=LR, FH=FH)
frame.Show(True)
def onButtonApplyParams(self, event):
result = wx.MessageBox('All rollovers will now be transformed and saved in the "dbrr" director.\nThis process may take several minutes to complete.\n\nOK to proceed?', 'Note:', wx.OK|wx.CANCEL)
if result==wx.OK:
self.metadata = DB.load_metadata(self.dir0)
PARAMS = self.metadata.load_registration_params()
dir0 = os.path.join(self.dir0, 'dbr')
dir1 = os.path.join(self.dir0, 'dbrr')
if not os.path.exists(dir1):
os.mkdir(dir1)
dialog = wx.ProgressDialog("", "Transforming pressure time series and saving to ./dbrr...", maximum=self.metadata.nRollovers, style = wx.PD_ELAPSED_TIME)
for i in range(self.metadata.nRollovers):
dialog.Update(i)
fname0 = os.path.join(dir0, 'rollover%05d.h5'%i)
fname1 = os.path.join(dir1, 'rollover%05d.h5'%i)
I = PM.load(fname0)
if np.any( np.abs(PARAMS[i] - [0,0,0,1]) > 1e-5 ):
I = PM.transformXYRS(I, PARAMS[i])
PM.save(fname1, I)
dialog.Destroy()
def onButtonSetProjectDirectory(self, event):
dir0 = None
dialog = wx.DirDialog(self.parent, 'Select a directory...', self.dir0, style=wx.DD_DEFAULT_STYLE)
if dialog.ShowModal() == wx.ID_OK:
dir0 = dialog.GetPath()
dialog.Destroy()
### load metadata:
if dir0!=None:
self.dir0 = dir0
self.settings.set_dir_project(dir0)
self.parent.statusbar.SetStatusText(dir0, 1)
for button in self.buttons[1:-1]:
button.Enable(True)
db = DB.PressureDatabaseInitializer(dir0)
db.check_initiated()
db.check_for_other_files()
if db.isinitiated:
self.metadata = DB.load_metadata(dir0)
self.metadata.dir0 = dir0
self.metadata.save()
else:
db.assemble_xml_filenames()
db.check_xml_filenames()
metadataXML = db.parse_xml_filenames()
result = wx.MessageBox('This project has not yet been initialized.\nInitialize now?\n\nNote: All XML files will be imported. This could take several minutes to complete.', 'Database initialization', wx.CANCEL | wx.OK)
if result==wx.OK:
importer = DB.XMLImporter(metadataXML, False)
dialog = wx.ProgressDialog("", "Importing XML files...", maximum=importer.nFiles, style = wx.PD_CAN_ABORT | wx.PD_ELAPSED_TIME)
keepGoing = True
count = 0
while keepGoing and (count < importer.nFiles):
keepGoing = dialog.Update(count)[0]
importer.filenum = count
importer.import_next()
count += 1
dialog.Destroy()
### save metadata:
metadataH5 = importer.finish()
metadataH5.save()
metadataH5.savexls()
metadataH5.savexls_subjmetadata()
metadataH5.save_template_choices()
def onButtonResize(self, event):
result = wx.MessageBox('Resizing image grids can take several minutes to complete. Click OK to proceed.', 'Image resizing', wx.CANCEL | wx.OK)
if result==wx.OK:
metadata = DB.load_metadata(self.dir0)
dialog = wx.ProgressDialog("", "Reading image sizes...", maximum=metadata.nRollovers, style = wx.PD_CAN_ABORT | wx.PD_ELAPSED_TIME)
dirDB = os.path.join(self.dir0, 'db')
dirDBr = os.path.join(self.dir0, 'dbr')
if not os.path.exists(dirDBr):
os.mkdir(dirDBr)
fnames = [os.path.join(dirDB, 'rollover%05d.h5'%i) for i in range(metadata.nRollovers)]
gs = PM.find_max_grid(fnames)
pad = 5
gs = [gs[0]+2*pad, gs[1]+2*pad]
keepGoing = dialog.Update(0, 'Resizing images...')[0]
count = 0
for i,fname in enumerate(fnames):
I = PM.load(fname)
I = PM.resize(I,gs)
keepGoing = dialog.Update(i)[0]
fname1 = os.path.join( dirDBr, os.path.split(fname)[1] )
PM.save(fname1, I)
dialog.Destroy()
def onButtonExportCOP(self, event):
dir0 = os.path.join(self.dir0, 'dbrr')
if not os.path.exists(dir0):
wx.MessageBox('Registration must be conducted and parameters applied before exporting COP trajectories.', 'Error:', wx.OK)
else:
dialog = wx.ProgressDialog("", "Extracting COP trajectories and saving to ./dbcop...", maximum=4*self.metadata.nSubj, style=wx.PD_ELAPSED_TIME)
self.metadata = DB.load_metadata(self.dir0)
dir1 = os.path.join(self.dir0, 'dbcop')
if not os.path.exists(dir1):
os.mkdir(dir1)
ii = 0
for subj in range(self.metadata.nSubj):
i = 0
for FH in [False,True]:
for LR in [False,True]:
rollovers = self.metadata.get_rollovers(subj, LR=LR, FH=FH, only_good=True)
II = self.metadata.load_rollovers(rollovers, dbdir='dbrr', max=False)
R = np.array([PM.extract_cop(I, interp=True, n=101) for I in II])
fname1 = os.path.join(dir1, 'subj%03d_cop%d.npy'%(subj,i))
np.save(fname1, R)
dialog.Update(ii)
i += 1
ii += 1
dialog.Destroy()