def upload(experimenter_id, date, mouse_id, filename):
experimenter = db.execute("SELECT name FROM lab_members WHERE id=%s",
(experimenter_id, ))[0][0]
mouse_name = db.execute("SELECT name FROM mice WHERE id=%s",
(mouse_id, ))[0][0]
currentdate = date.replace('-', '.')
print(currentdate)
if os.environ['COMPUTERNAME'] == 'ARMSTRONG': # Kyle's computer
pathTo2P = 'X:/Recordings/2P/' + experimenter + '/' + currentdate + '/' + mouse_name + '/'
if os.path.isdir(pathTo2P) is False:
pathTo2P = 'C:/Users/kyle/Desktop/recordings/' + experimenter + '/' + currentdate + '/' + mouse_name + '/'
pathToCond = 'C:/Users/kyle/Dropbox/Data/Conditions/2P/' + time.strftime(
'%d-%b-%Y', time.strptime(currentdate, '%Y.%m.%d')) + '/'
elif os.environ['COMPUTERNAME'] == 'MOM1': # Aquisiton Computer
pathTo2P = 'D:/data/' + experimenter + '/' + currentdate + '/' + mouse_name + '/'
pathToCond = 'C:/Users/MOM1/Documents/Dropbox/Data/Conditions/2P/' + time.strftime(
'%d-%b-%Y', time.strptime(currentdate, '%Y.%m.%d')) + '/'
if os.path.isdir(pathTo2P) is False:
print('There is no directory {}'.format(pathTo2P))
return False
elif os.path.isdir(pathToCond) is False:
print('There is no directory {}'.format(pathToCond))
return False
cond_files = os.listdir(pathToCond)
print('pathToCond: {}'.format(pathToCond))
for cond_file in cond_files:
print('COND FILE: {}'.format(cond_file))
base_name, ext = os.path.splitext(cond_file)
print('pathTo2P: {}'.format((pathTo2P + base_name + '.tif')))
if os.path.exists(pathTo2P +
cond_file) and os.path.exists(pathTo2P + base_name +
'.tif'):
c = scipy.io.loadmat(pathToCond + cond_file)
try:
c2 = scipy.io.loadmat(pathTo2P + cond_file)
# debug.enter()
except IOError:
print(
"You need the 2P conditions file as well as the stimulus conditions file"
)
if 'meta_data' in c.keys():
dd = files2db(c, c2)
dd['date'] = time.strftime(
'%Y-%m-%d', time.strptime(currentdate, '%Y.%m.%d'))
dd['filename'] = base_name
dd['experimenter_id'] = experimenter_id
dd['mouse_id'] = mouse_id
add2db(dd)
print('All files uploaded to ED successfully')
def add2db(dd):
print('Mouse id = {}'.format(dd['mouse_id']))
ans = db.execute(
"""
SELECT mice.id FROM experiments
LEFT JOIN mice ON mice.id=mouse_id
LEFT JOIN lab_members ON experiments.lab_member_id=lab_members.id
WHERE lab_members.id=%s
AND experiments.date=%s
AND mice.id=%s""", (dd['experimenter_id'], dd['date'], dd['mouse_id']))
if ans == []:
print('No glams entry for animal on {}'.format(dd['date']))
return 1
if len(ans) > 1:
print(
"More than one experiment was done on this mouse today. This is ambiguous."
)
return 1
dd['mouse_id'] = ans[0][0]
db.config['database'] = 'ed'
ans2 = db.execute(
"""SELECT mouse_id, experimenter_id, date, filename FROM 2P_visual_stims WHERE mouse_id=%s AND experimenter_id=%s AND date=%s AND filename=%s""",
(dd['mouse_id'], dd['experimenter_id'], dd['date'], dd['filename']))
if ans2 != []: #if the entry is already in the database
print('File {} from {} to database already exists. File not added.'.
format(dd['filename'], dd['date']))
db.config['database'] = 'glams'
return 1
print('this works')
cols = ''
parameters = []
for key in dd.keys():
cols += " {}=%s,".format(key)
parameters.append(dd[key])
cols = cols[:-1]
parameters = tuple(parameters)
db.execute('INSERT INTO 2P_visual_stims SET {}'.format(cols), parameters)
db.config['database'] = 'glams'
print('Added file {} from {} to database.'.format(dd['filename'],
dd['date']))
def getExperiments(lab_member_name):
query = """SELECT r.date as experiment_date,
m.name AS mousename,
m.DOB,
DATEDIFF(r.date,m.DOB) AS age,
r.description,
r.notes
FROM mice as m
LEFT JOIN experiments as r ON m.id=r.mouse_id
LEFT JOIN lab_members ON lab_members.id=r.lab_member_id
WHERE lab_members.name='{0}'
ORDER BY r.date""".format(lab_member_name)
experiments = db.execute(query)
return experiments
def getExperiments(lab_member_name):
query="""SELECT r.date as experiment_date,
m.name AS mousename,
m.DOB,
DATEDIFF(r.date,m.DOB) AS age,
r.description,
r.notes
FROM mice as m
LEFT JOIN experiments as r ON m.id=r.mouse_id
LEFT JOIN lab_members ON lab_members.id=r.lab_member_id
WHERE lab_members.name='{0}'
ORDER BY r.date""".format(lab_member_name)
experiments=db.execute(query)
return experiments
def saveResults(self):
if self.persistant is None:
self.alert = QtGui.QMessageBox.information(
self, 'Save Results',
"You must load a file in order to save the results.")
else:
self.persistant['ROIs'] = [
r.getpersistant() for r in self.tiffFig.rois
] #This creates a list with the numbers of interest (determined by getpersistant() for each ROI.
p = pickle.dumps(self.persistant)
ids = [
self.persistant['mouse_id'], self.persistant['experimenter_id'],
self.persistant['date'], self.persistant['filename']
] #The four components of an ID (moud, experimenter, date, and filename) make a file unique.
db.config['database'] = 'ed'
ans = db.execute(
"SELECT * FROM analysis2p WHERE mouse_id=%s AND experimenter_id=%s AND date=%s and filename=%s",
tuple(ids)
) #This exists to check whether this file has been analyzed before
date_analyzed = time.strftime('%Y-%m-%d', time.localtime())
ids.insert(0, date_analyzed)
ids.insert(1, p)
if len(ans) > 0:
db.execute(
"UPDATE analysis2p SET date_analyzed=%s, data=%s WHERE mouse_id=%s AND experimenter_id=%s AND date=%s AND filename=%s",
tuple(ids))
self.statusBar().showMessage(
"Results were successfully saved (Overwrote previous results)."
)
else:
db.execute(
"INSERT INTO analysis2p SET date_analyzed=%s, data=%s, mouse_id=%s, experimenter_id=%s, date=%s, filename=%s",
tuple(ids))
self.statusBar().showMessage("Results were successfully saved.")
db.config['database'] = 'glams'
def getTimedMatings():
query = """SELECT m.name AS mousename, h1.start_date, h1.end_date, c1.name AS homecage, c2.name AS breedingcage, DATEDIFF(NOW(),h1.start_date) AS daysSinceMating
FROM mice as m
LEFT JOIN housing as h1 ON h1.mouse_id=m.id
LEFT JOIN housing as h2 ON h2.mouse_id=m.id
LEFT JOIN housing as h3 ON h3.mouse_id=m.id
LEFT JOIN care_taker ON care_taker.cage_id=h1.cage_id
LEFT JOIN lab_members ON lab_members.id=care_taker.lab_member_id
LEFT JOIN cages AS c1 ON c1.id=h1.cage_id
LEFT JOIN cages AS c2 ON c2.id=h2.cage_id
WHERE DATEDIFF(h1.end_date,h1.start_date)=1
AND h2.cage_id=h3.cage_id
AND h2.end_date=h1.start_date
AND h3.start_date=h1.end_date
AND DATEDIFF(NOW(),h1.start_date)<21
ORDER BY c1.name"""
matings = db.execute(query)
return matings
def getTimedMatings():
query="""SELECT m.name AS mousename, h1.start_date, h1.end_date, c1.name AS homecage, c2.name AS breedingcage, DATEDIFF(NOW(),h1.start_date) AS daysSinceMating
FROM mice as m
LEFT JOIN housing as h1 ON h1.mouse_id=m.id
LEFT JOIN housing as h2 ON h2.mouse_id=m.id
LEFT JOIN housing as h3 ON h3.mouse_id=m.id
LEFT JOIN care_taker ON care_taker.cage_id=h1.cage_id
LEFT JOIN lab_members ON lab_members.id=care_taker.lab_member_id
LEFT JOIN cages AS c1 ON c1.id=h1.cage_id
LEFT JOIN cages AS c2 ON c2.id=h2.cage_id
WHERE DATEDIFF(h1.end_date,h1.start_date)=1
AND h2.cage_id=h3.cage_id
AND h2.end_date=h1.start_date
AND h3.start_date=h1.end_date
AND DATEDIFF(NOW(),h1.start_date)<21
ORDER BY c1.name"""
matings=db.execute(query)
return matings
def getInfoFromPath(path):
'''
This uses the path to return a dictionary containing:
date - a python date object
datestr - a string of the date of the format 2014-01-31
experimenter - a string with the experimenter name as it is in GLAMS
experimenter_id - an int with the experimenter id as it is in GLAMS
mouse_name - a string with the mouse name as it is in GLAMS. If the mouse_name is not in the path, it is a 'None' object
mouse_id an int with the experimenter id as it is in GLAMS.
filename - the name of the tif file without the path or the extension
The path must be either of the form
"somewhere/experimenter/date/mouse_name/filename.tif"
or
"somewhere/experimenter/year.month.day/filename.tif"
If there is no mouse_name in the path, the experimenter, date, and filename must be unique in ED (the Experiment Database). If it is not, an error will be thrown.
'''
d = dict()
d['path'] = path
path = path.split('/')
d['filename'] = path[-1].split('.tif')[0]
try:
d['date'] = time.strptime(path[-2], '%Y.%m.%d')
except ValueError: #if index -2 is a mousename and not a date
d['mouse_name'] = path[-2]
d['date'] = time.strptime(path[-3], '%Y.%m.%d')
mnameExists = True
else:
d['mouse_name'] = None
mnameExists = False
d['datestr'] = time.strftime('%Y-%m-%d', d['date'])
if mnameExists:
d['experimenter'] = path[-4]
else:
d['experimenter'] = path[-3]
# debug.enter()
if mnameExists is False:
ans = db.execute(
"""
SELECT mice.id, lab_members.id AS experimenter_id, mice.name AS mouse_name
FROM experiments
LEFT JOIN mice ON mice.id=mouse_id
LEFT JOIN lab_members ON experiments.lab_member_id=lab_members.id
WHERE lab_members.name=%s
AND experiments.date=%s""", (d['experimenter'], d['datestr']))
if ans == []:
print('No GLAMS entry for an experiment by {} on {}'.format(
d['experimenter'], d['datestr']))
return False
if len(ans) > 1:
print(
'Multiple GLAMS entries for experiments by {} on {}. Add a mouse_name to the path of this file.'
.format(d['experimenter'], d['datestr']))
return False
else:
d['mouse_name'] = ans[0][2]
else:
ans = db.execute(
"""
SELECT mice.id, lab_members.id AS experimenter_id
FROM experiments
LEFT JOIN mice ON mice.id=mouse_id
LEFT JOIN lab_members ON experiments.lab_member_id=lab_members.id
WHERE lab_members.name=%s
AND experiments.date=%s
AND mice.name=%s""",
(d['experimenter'], d['datestr'], d['mouse_name']))
if ans == []:
print('No glams entry for an experiment by {} on mouse {} on {}'.
format(d['experimenter'], d['mouse_name'], d['date']))
return False
d['mouse_id'] = ans[0][0]
d['experimenter_id'] = ans[0][1]
print(
'Experimenter = {}\nDate of Recording = {}\nMouse name = {}\nFile name = {}'
.format(d['experimenter'], d['datestr'], d['mouse_name'],
d['filename']))
return d
def loadfile(maingui):
# remove old figures if there are any
try:
maingui.tiffFig.traceFig.deleteLater()
maingui.tiffFig.responseFig.deleteLater()
maingui.roi_table.deleteLater()
maingui.rmax_by_sfreq.deleteLater()
except Exception:
pass
settings = maingui.settings
#### get conditions from ED ####
d = getInfoFromPath(settings.d['filename'])
maingui.persistant = dict()
maingui.persistant['experimenter_id'] = d['experimenter_id']
maingui.persistant['date'] = d['datestr']
maingui.persistant['mouse_id'] = d['mouse_id']
maingui.persistant['filename'] = d['filename']
if d is False: #if there was an error loading the conditions file
maingui.conditions = None
else:
maingui.conditions = getConditions(
experimenter_id=d['experimenter_id'],
date=d['datestr'],
mouse_id=d['mouse_id'],
filename=d['filename'])
### try loading previous results from ED ###
ids = [
maingui.persistant['mouse_id'], maingui.persistant['experimenter_id'],
maingui.persistant['date'], maingui.persistant['filename']
]
db.config['database'] = 'ed'
ans = db.execute(
"SELECT data, id FROM analysis2p WHERE mouse_id=%s AND experimenter_id=%s AND date=%s and filename=%s",
tuple(ids))
db.config['database'] = 'glams'
if len(ans) > 0:
old_persistant = pickle.loads(ans[0][0])
maingui.persistant = dict(maingui.persistant.items() +
old_persistant.items())
maingui.persistant['id'] = ans[0][1]
print('Found persistent data on ED')
else:
maingui.persistant['id'] = None
maingui.persistant = dict(maingui.persistant.items() + dict.fromkeys(
['motionVectors', 'ROIs', 'neuropil_radius', 'alpha']).items())
print(
'Persistent data on ED not found. This file has not been loaded into ceilingfaan before.'
)
maingui.statusBar().showMessage('Loading tiff')
t = time.time()
tif = tifffile.TIFFfile(settings.d['filename'])
tiffstack = tif.asarray()
tif.close()
tiffstack = np.transpose(tiffstack, (0, 2, 1))
maingui.statusBar().showMessage(
'Tiff successfully loaded ({} s)'.format(time.time() - t))
maingui.roi_table = roi_table.make_widget(maingui, show=True)
maingui.rmax_by_sfreq = TuningCurveCanvas((536, 33, 446, 300))
maingui.rmax_by_sfreq.show()
maingui.stats = StatsWindow.from_geo(maingui, 680, 373, 230, 660)
maingui.stats.show()
# maingui.rmax_by_sfreq = RMaxBySpatialFrequencyFig()
# maingui.rmax_by_sfreq.show()
## maingui.npplot = maingui.neuropil_mask.addPlot()
## maingui.npplot.hideAxis('left')
## maingui.npplot.hideAxis('bottom')
##########################################################
# Injected by Hyungtae Kim <*****@*****.**>, in Nov 2014, Feb 2015
# organize a menu to select a specific frequency based on conditions.
#
def on_tfreq_change(maingui, agroup):
checked = agroup.checkedAction()
checked_index = agroup.children().index(checked)
maingui.tiffFig.temporal_frequency_changed(checked_index)
def on_sfreq_change(maingui, agroup):
checked = agroup.checkedAction()
checked_index = agroup.children().index(checked)
maingui.tiffFig.spatial_frequency_changed(checked_index)
sf_agroup = maingui.sfreq_action_group
sf_handler = partial(on_sfreq_change, maingui, sf_agroup)
tf_agroup = maingui.tfreq_action_group
tf_handler = partial(on_tfreq_change, maingui, tf_agroup)
for action in sf_agroup.children():
sf_agroup.removeAction(action)
for action in tf_agroup.children():
tf_agroup.removeAction(action)
if maingui.conditions:
maingui.sfreq_meta = SpatialFrequencyMeta(maingui.conditions)
for index, text in enumerate(map(str,
maingui.sfreq_meta.sfrequencies)):
if_first = not index
action = QAction(text, sf_agroup, checkable=True, checked=if_first)
sf_agroup.addAction(action)
maingui.sfreq_menu.addAction(action)
action.triggered[()].connect(sf_handler)
for index, text in enumerate(map(str,
maingui.sfreq_meta.tfrequencies)):
if_first = not index
action = QAction(text, tf_agroup, checkable=True, checked=if_first)
tf_agroup.addAction(action)
maingui.tfreq_menu.addAction(action)
action.triggered[()].connect(tf_handler)
else:
maingui.sfreq_meta = None
channels = []
if settings.d['nChannels'] == 1:
channels.append(tiffstack)
(mt, my, mx) = shape(channels[0])
tiffstack = np.concatenate(
(channels[0][..., np.newaxis], np.zeros((mt, my, mx, 2))),
axis=3) #this always assumes the only color is green
elif settings.d['nChannels'] == 2:
channels.append(tiffstack[0::2])
channels.append(tiffstack[1::2])
(mt, my, mx) = shape(channels[0])
arr1 = channels[0][..., np.newaxis]
arr2 = channels[1][..., np.newaxis]
arr3 = np.zeros((mt, my, mx, 1))
tiffstack = np.concatenate(
(arr1, arr2, arr3),
axis=3) #this always assumes the only two colors are red and green
elif settings.d['nChannels'] == 3:
channels.append(tiffstack[0::3])
channels.append(tiffstack[1::3])
channels.append(tiffstack[2::3])
tiffstack = np.concatenate(
(channels[0][..., np.newaxis], channels[1][..., np.newaxis],
channels[2][..., np.newaxis]),
axis=3
) #this always assumes the only three colors are red,green, and blue in that order
COI = channels[settings.d['channelOfInterest'] - 1] #channel of interest
(mt, my, mx) = shape(COI)
if settings.d['motionCorrect']: #True or False depending on user settings
maingui.statusBar().showMessage('Performing motion correction...')
t = time.time()
if maingui.persistant['motionVectors'] is None:
print 'motion vector not found, get drift !'
maingui.persistant['motionVectors'] = getdrift3(COI)
print 'driftcorrect...',
tiffstack = driftcorrect(tiffstack,
maingui.persistant['motionVectors'])
print 'done !'
maingui.statusBar().showMessage(
'Finished motion correction ({} seconds)'.format(time.time() - t))
else:
maingui.statusBar().showMessage('Motion Correction is Off')
maingui.persistant['motionVectors'] = None
tiffFig = TiffFig(
tiffstack, maingui
) # activates the movie display window and the response analysis windows
# SPG 072414 writes out motion corrected file to matlab where we can save each channel as a tifstack. replace this with python
# code once we figure out which python TIFF writer to use
# if settings.d['saveMotionCorrectedTIFF']==True:
# # tiffstack.save(settings.d['filename']+'motionCorrected.tif')
# # tifffile.imsave(settings.d['filename']+'motionCorrected.tif',tiffstack, compress=6)
# matd=dict();
# matd['tiffStack']=tiffstack;
# scipy.io.savemat(settings.d['filename']+'motionCorrected.tif',matd);
return tiffFig
def getaName():
lab_members = db.execute("SELECT name FROM lab_members")
return lab_members[0][0]
def main():
mice=db.execute("SELECT name FROM mice")
print(mice)
def getaName():
lab_members=db.execute("SELECT name FROM lab_members")
return lab_members[0][0]
def main():
mice = db.execute("SELECT name FROM mice")
print(mice)