def enableNext(bid, j):
[v, s, p] = bid.split(".")
try:
nextBtn = btn_node("%s.%s.%d" % (v, s, int(p) + 1), j)
except LookupError: ## done with this step
try:
nextBtn = btn_node("%s.%d.%d" % (v, int(s) + 1, 0), j)
except LookupError: ## done with this visit
vNode = get_visit(bid, j)
lib.set_node(vNode, True, jlib.VCOMPLETE)
return int(v) + 1
## we have the next valid button: enable it!
## ... unless we're in redo-mode: skip completed steps until we've resumed
resume = lib.get_node(j, jlib.RESUME)
if resume: # redo-mode!
if compareBids(resume, nextBtn["id"]): # we've caught up to the resume point
lib.set_node(j, None, jlib.RESUME) # end redo-mode
lib.set_here(nextBtn, "disabled", False) # enable as normal
else: # stay in redo-mode
if lib.get_node(nextBtn, "time") == "": # not stamped yet, so enable
lib.set_here(nextBtn, "disabled", False)
else: # timestamped; this was complete before redo began.
# don't enable; rather, advance progress & skip to next-next
nextID = lib.get_node(nextBtn, "id")
setProgress(nextID, get_visit(bid, j))
return enableNext(nextID, j)
else: # no redo occurring, normal enable
lib.set_here(nextBtn, "disabled", False)
return int(v)
def processLogin(self):
subject = self.subject
print 'SUBJECT['+ subject+']'
self.mySubjectDir = j.checkSubjDir(subject)
j.dirStructure(subject) # verify/create subject's directory structure (visits, etc.)
self.jsonpath = os.path.join(self.mySubjectDir,
"%s_experiment_info.json" % subject)
if os.path.exists(self.jsonpath):
self.json = lib.load_json(self.jsonpath)
self.json['flotscript'] = ''
if 'flotscript_header' in self.json:
del self.json['flotscript_header']
else:
lib.set_node(self.json, subject, j.SUBJID) ## get a fresh json_template
## find the next incomplete visit (if study complete, display final visit)
for v in range(j.NUM_VISITS):
self.setTab(v)
if not lib.get_node(self.json, self.vNodePath + j.VCOMPLETE):
break
visit = v
# handle subject's group assignment and create visit/session dir based on group, if needed.
group = lib.get_node(self.json, j.GROUP)
if not group == "":
### create & populate session dir
self.visitDir, correctVisit = j.checkVisitDir(subject, visit, group, self.json)
if not correctVisit == visit:
self.subjectMoved("<b>Cannot move on to next visit without ROI masks!</b>", "false")
self.setTab(correctVisit)
return self.renderAndSave() # saves the json, and renders the page
else:
return self.modalthing() # render modal to assign group -> call setgroup() -> save json & render normally
def completionChecks(self):
tab = self.TabID
vComplete = lib.get_node(self.json,self.vNodePath + j.VCOMPLETE)
print "complete:", vComplete,
if vComplete:
return
progress = lib.get_node(self.json, self.vNodePath + j.VPROGRESS)
print "... progress:",progress, "tab:",tab
if progress == "": ## activate first step, deactivate all else
if (tab == 0):
[bt.enableOnly(self.json, t, None) for t in range(1,len(j.VISIT_LIST))]
bt.enableOnly(self.json, tab, 'first')
else:
prevVNodePath = self.vNodePath[:-2] + str(tab-1) + ":"
lastVComplete = lib.get_node(self.json, prevVNodePath + j.VCOMPLETE)
if lastVComplete:
bt.enableOnly(self.json, tab, 'first')
else:
bt.enableOnly(self.json, tab, None)
else:
activeVisit = bt.enableNext(progress,self.json)
if not activeVisit == tab:
bt.enableOnly(self.json, tab, None)
if activeVisit < j.NUM_VISITS:
bt.enableOnly(self.json, activeVisit, 'first')
else:
self.subjectMoved("<b>All visits complete!</b>", "false")
return
def nameLogfile(node,subject,useInfo=None):
"""
Out: absolute path where stdout/stderr logfile should go
"""
# error check: useInfo has 'run','history'; node has 'action', 'id'
if not useInfo: ## allow us to (optionally) use a different btn's info
useInfo=node ## use this btn's info by default
run = useInfo['run']
timeStr = time.strftime("_%b%d_%H%M%S_",time.localtime(float(lib.get_node(useInfo,'history:-1'))))
action = node['action']
tab = int(lib.get_node(node,'id')[0])
filename = str(run) + timeStr + action + '.log'
return os.path.abspath(os.path.join(lib.SUBJS, subject, "session%d"%tab, filename))
def checkVisitDir(subject,visit,group,myJson):
v = int(visit)
maxV = len(VISIT_LIST) ## off-by-one error???
if v > maxV: ##obo danger
print "ERROR checkVisitDir: requested",v, "but the max visit number is", maxV
raise Exception("Invalid visit number requested.")
if v < 0: ## supports visits[-1] indexing
v = maxV + 1 + v
subjDir = checkSubjDir(subject) # checks/creates subjDir
myVisitDir = getVisitDir(subject, v)
if not os.path.exists(myVisitDir):
raise OSError("Can't find this visit directory! %s"%myVisitDir)
vType = get_node(bt.get_visit(v, myJson), VTYPE)
# for realtime visits, verify murfi templates (in 'scripts' directory) exist
if vType == 'realtime':
# first check that localizer masks are present
if not os.path.exists(os.path.join(subjDir, 'mask')):
print "You can't do a realtime run until there are subject masks!"
v = 0
return getVisitDir(subject, v), v
murfiDir = os.path.abspath(os.path.join(myVisitDir, "scripts"))
if not os.path.exists(murfiDir):
### this is dumb. i should make it an importable library.
print "Trying to create rt session for visit", v
subprocess.Popen(["python", "createRtSession.py", subject, str(v), 'none', group], cwd=RTSCRIPTSDIR)
return myVisitDir, v
def doMakoLogin(self,subject=None,visit=None):
self.subject = subject ## keep this accessible to other methods
self.mySubjectDir = j.checkSubjDir(subject)
self.jsonpath = os.path.join(self.mySubjectDir, "%s_experiment_info.json"%subject)
if os.path.exists(self.jsonpath):
self.json = lib.load_json(self.jsonpath)
else:
lib.set_node(self.json,subject,j.SUBJID) ## get a fresh json_template
visit = lib.get_node(self.json,j.TAB)
self.setTab(visit) # activates the tab
# handle subject's group assignment and create visit/session dir based on group, if needed.
group = lib.get_node(self.json, j.GROUP)
if not group == "":
self.visitDir = j.checkVisitDir(subject,visit,group, self.json) ### create & populate session dir
return self.renderAndSave() # saves the json, and renders the page
else:
return self.modalthing() # render modal to assign group -> call setgroup() -> save json & render normally
def btn_node(bid,j):
"""
Helper designed for MakoRoot.formHandler().
Returns a dict of button properties for the desired button.
In: * bid (str), "x.y.z"
* j (dict-like), MakoRoot.json
Out: * node (dict-like), subnode of j, for that button
"""
[v,s,p] = bid.split('.')
return lib.get_node(j,['protocol',v,'steps',s,'parts',p])
def get_visit(info,j):
if isinstance(info,str): ## info is a buttonID, like v.s.p
visit = int(info[0])
elif isinstance(info,unicode): ## also probably a buttonID?
visit = int(info[0])
elif isinstance(info,int): ## info is just a visit number
visit = info
else:
print "info in get_visit:", info
raise TypeError("get_visit: Didn't expect a %s"%(type(info)))
return lib.get_node(j, [jlib.FULLSTUDY,visit])
def parent_node(bid,j):
"""
Helper that get's a button's parent-step's parts.
Returns the parent node of a button, which must be the "parts"
list of the step that the button is a part of. There may be only
one part in the list.
In: * bid (str), "x.y.z"
* j (dict-like), MakoRoot.json
Out: * parent (list), subnode of j, for that button
"""
[v,s,p] = bid.split('.') ## won't be using p
return lib.get_node(j, ['protocol',v,'steps',s,'parts'])
def checkPsychoDone(subject, node):
tab = int(lib.get_node(node,'id')[0])
expName = os.path.splitext(os.path.basename(node['file']))[0]
filename = expName + getTimestamp(node, -2) + 'trials.psydat'
doneFile = os.path.abspath(os.path.join(lib.SUBJS, subject, "session%d"%tab, 'ltTaskData', expName, filename))
print "Psychopy complete? Checking", doneFile
if os.path.exists(doneFile):
datFile = fromFile(doneFile)
print "Found .psydat file. Collected",datFile.thisN, "trials, so finished is",datFile.finished
return datFile.finished
else:
return False
def sib_node(bid,j,z):
"""
Button groups consist of sibling buttons. Get sibling z for the
button bid.
Returns a dict of button properties for the desired sibling button.
In: * bid (str), eg "x.y.z"
* j (dict-like), MakoRoot.json
* z (int/str), indicating which sibling to return
Out: * node (dict-like), subnode of j, for the sibling button
"""
[v,s,p] = bid.split('.')
return lib.get_node(j,['protocol',v,'steps',s,'parts',z])
def movementRedo(j, tab):
## Use this visit's progress to figure out what things to redo.
## Collaborate with enableNext() to use timestamps as a high-water mark.
## j (dict) = full json for the subject
## tab (int) = visit/session number
vNode = get_visit(tab, j)
vBids = visitBids(tab, j) ## full, ordered list of all button ids for this visit
progress = getProgress(vNode)
currentBid = vBids[vBids.index(progress) + 1] ## for current step (after progress)
## 1. build prereq button id list
# 1.1 get base prereqs, plus prereqs based on current step's action keyword
action = lib.get_node(btn_node(currentBid, j), "action")
prereqs = []
for btn in [btn_node(bid, j) for bid in visitBids(tab, j)]:
if btn.has_key("prereqFor"):
prfor = btn["prereqFor"].split(".") # some prereqs are '.'-joined
if ("all" in prfor) or (action in prfor):
prereqs.append(btn["id"])
# 1.2 get all siblings of the current step
sibs = [lib.get_node(sib, "id") for sib in parent_node(currentBid, j)]
prereqs.extend(sibs)
# 2. prepare prereqs for redo: clear all tstamps, uncheck checkboxes.
for prereq in prereqs:
prNode = btn_node(prereq, j)
clearTimeStamp(prNode)
if lib.get_node(prNode, "action") == "": # it's a checkbox
lib.set_here(prNode, "checked", False) # clear checkboxes
# 3. save progress to study-wide resume pointer, unless we're restarting a redo.
resume = lib.get_node(j, jlib.RESUME)
if resume:
pass ## restarting redo-mode due to another movement
else: ## enter fresh redo-mode
lib.set_node(j, progress, jlib.RESUME)
# 4. reset progress so that the first prereq is the next thing to happen.
vBids.insert(0, "") # if 1st prereq is tab.0.0, then progress = "" (as expected)
resetBid = vBids[vBids.index(prereqs[0]) - 1]
setProgress(resetBid, vNode)
return
def updateProgress(self,bid):
"""
Only call this once an action (or structural scan) is done.
"""
# do nothing if progress > bid (because we're redoing something)
curProg= lib.get_node(self.json, self.vNodePath + j.VPROGRESS)
if curProg == "": # beginning of a visit, or we're in redo mode.
bt.setProgress(bid, bt.get_visit(bid,self.json))
elif bt.compareBids(curProg, bid): # step
print "new progress will be",bid
bt.setProgress(bid, bt.get_visit(bid,self.json))
else:
print "completed", bid, ", but that's less than", curProg
return
def makoRealtimeStim(self, btn_value, node):
murfNode = bt.sib_node(node['id'], self.json, 0)
stimLog = bt.nameLogfile(node, self.subject, murfNode)
self.run = murfNode['run'] ## in case of accidental logout
self.flotJavascript()
# based on group, use proper stimulus file
group = lib.get_node(self.json, j.GROUP)
if group == "high":
psychofile = j.HIFILE
elif group == "low":
psychofile = j.LOFILE
lib.set_here(node, 'file', psychofile) # record which stimulus file was used
# ready to launch!
self.stimProc, h = lib.doStim(self.subject, self.TabID, self.run, stimLog, psychofile,self.json["study_info"]["group"])
lib.set_here(node,'disabled', True) # this button only launches. 'End Murfi' cleans up
return
def subjectMoved(self, reason, moved="false"):
print self.TabID, reason, moved
## timestamp and store comment
infoNode = lib.get_node(self.json, ['protocol',self.TabID,'visit_info'])
bt.timeStamp(infoNode)
infoNode['comments'].append(reason)
## determine which steps need to be redone
if moved == "true":
## QUESTION: should we be on an active visit only?
## enable & clear printed timestamp on localizers & test equipment
bt.movementRedo(self.json, self.TabID)
## REMINDER: on functional runs, they should get to hit "end" (minor bug)
elif moved == "false":
pass ## just adding the comment to visit_info
else:
raise Exception("Invalid value for 'moved' from radio button!")
return self.renderAndSave()
def dirStructure(subject):
# subject (str): subject id
for v, vNode in enumerate(VISIT_LIST):
vType = get_node(vNode, VTYPE)
vDir = getVisitDir(subject, v)
if vType == "prepost":
if os.path.exists(vDir):
pass
else:
os.mkdir(vDir)
elif vType == "realtime":
rtDataDir = os.path.abspath(os.path.join(vDir, "data"))
if not os.path.exists(rtDataDir):
os.makedirs(rtDataDir)
else:
print "Didn't understand visit type", vType, "for visit number", v
raise Exception("Subject's directory structure creation/verification failed.")
return
def rtDone(j, bid):
# Purpose: When an RT run completes, this advances the "progress" key
# to the last part of the RT step, so that enableNext can enable the
# next step or next visit.
# This is a helper function for handling an "End Murfi" buttonpress. Nothing
# else should call it.
# Inputs:
# j (dict) = full json the subject
# bid (str) = "x.y.z", as above
node = btn_node(bid, j)
lib.set_here(node, 'done', True)
# disable all sibling parts
parent = parent_node(bid, j)
for p in range(0, len(parent)):
lib.set_here(parent[p], 'disabled', True)
# progress is set to button ID of the last part of this step.
lastID = lib.get_node(parent, ['-1', 'id'])
setProgress(lastID, get_visit(bid, j))
def flotSetup(subject):
flotcalls = []
actTempl = os.path.join(os.path.abspath("."), "template_active.json")
refTempl = os.path.join(os.path.abspath("."), "template_reference.json")
u = os.path.expanduser('~')
for v, vNode in enumerate(VISIT_LIST):
vType = get_node(vNode, VTYPE)
vDir = getVisitDir(subject, v)
if vType == "realtime":
rtDataDir = os.path.abspath(os.path.join(vDir, "data"))
for run in range(1, STUDY_INFO['runsPerRtVisit'] + 1):
filebase = "run%03d_"%run
actFile = os.path.join(rtDataDir, filebase + "active.json")
refFile = os.path.join(rtDataDir, filebase + "reference.json")
placeholder = '$("#rtgraph%d_%d")' % (v, run)
flotcalls.append('flotplot("%s", "%s", %s);' % (os.path.relpath(actFile, u),
os.path.relpath(refFile, u), placeholder))
if not os.path.exists(actFile):
shutil.copy(actTempl, os.path.join(rtDataDir, actFile))
if not os.path.exists(refFile):
shutil.copy(refTempl, os.path.join(rtDataDir, refFile))
return flotcalls
def checkVisitDir(subject,visit,group,myJson):
print SUBJS
print RTSCRIPTSDIR
v = int(visit)
maxV = len(VISIT_LIST) ## off-by-one error???
if v > maxV: ##obo danger
print "ERROR checkVisitDir: requested",v, "but the max visit number is", maxV
raise Exception("Invalid visit number requested.")
if v < 0: ## supports visits[-1] indexing
v = maxV + 1 + v
myVisitDir = os.path.abspath(os.path.join(SUBJS,subject,'session%d'%v))
print myVisitDir
if not os.path.exists(myVisitDir):
if not os.path.exists(checkSubjDir(subject)):
raise OSError("Can't find directory for this subject.")
else:
os.mkdir(myVisitDir)
vType = get_node(myJson, "%s:%d:%s"%(FULLSTUDY, v, VTYPE))
if vType == 'realtime':
os.mkdir(os.path.join(myVisitDir, 'data')) ## psychopy data directory.
### this is dumb. i should make it an importable library.
print "Trying to create rt session for visit", visit
subprocess.Popen(["python", "createRtSession.py", subject, str(v), 'none', group], cwd=RTSCRIPTSDIR)
return myVisitDir
def subjectMoved(reason):
print self.tab, reason
infoNode = lib.get_node(self.json, ['Protocol',self.tab,'visit_info'])
bt.timeStamp(infoNode)
infoNode['comments'].append(reason)
return self.renderAndSave()
def getTimestamp(node,index=-1): ## return time formatted like psychopy.data.getDateStr (but not unicode)
return time.strftime("%Y_%b_%d_%H%M",time.localtime(float(lib.get_node(node,'history:%d'%index))))
def visitBids(tab, j):
vNode = get_visit(int(tab), j)
vBids = []
for s in range(0, len(vNode['steps'])):
vBids.extend([str(p) for p in lib.get_node(vNode,"steps:%d:parts:*:id"%s)])
return vBids
def getProgress(visitNode):
return lib.get_node(visitNode, jlib.VPROGRESS)