Understanding PsychoPy codes for trialHandler and responses - psychopy

I am new to coding, and would like help in understanding the script used by the PsychoPy program.
To be more specific, I would like to understand the codes that are in line 6 to 15. I am aware that this is used to manage the multiple trials, but I am hoping someone can help me clarify those bits? I also noted that removing the codes from line 6-8 doesn't change the experiment, but removing the codes from line 10-15 essentially stop the experiment from running.
trialsAll = data.TrialHandler(trialList=data.importConditions('trialType.xlsx'), nReps=10, method='random', name='trialsAll', dataTypes='corr')
thisExp = data.ExperimentHandler(name='Ours')
thisExp.addLoop(trialsAll) #adds a loop to the experiment
thisTrial = trialsAll.trialList[0]
if thisTrial != None:
for paramName in thisTrial.keys():
exec(paramName + '= thisTrial.' + paramName)
# Loop through trials
for thisTrial in trialsAll:
currentLoop=trialsAll
if thisTrial != None:
for paramName in thisTrial.keys():
exec(paramName + '=thisTrial.' + paramName)
My second question would be about getting responses. Is there a reason that thisResp is equalled to None?
#get response
thisResp=None
while thisResp==None:
allKeys=event.waitKeys()
Thanks a lot for any help. I appreciate it.
Regards,
Cash

if thisTrial != None:
for paramName in thisTrial.keys():
exec(paramName + '= thisTrial.' + paramName)
This code allows the use of abbreviations. For example, say your conditions file has a field called 'angle', you can refer to this directly rather than via the keys of that trial's dictionary (e.g. thisTrial['angle'] ) or using dot notation ( thisTrial.angle ). i.e., in this example:
angle = thisTrial.angle
for thisTrial in trialsAll:
is fundamental to running a psychoPy trial loop. It will cycle though each trial that is contained in the TrialHandler object that is created to manage trials, connected to a given conditions file.
#get response
thisResp=None
while thisResp==None:
allKeys=event.waitKeys()
The line 'while thisResp==None:' requires that the variable 'thisResp' actually exists if we are going to be able to check its value. So in the immediately preceding line, it is created and given an initial null value so that the next line will run OK. Note that at this stage, it is just an arbitrary variable, which doesn't have any actual connection to the subject's response. That will presumably occur later in the code, when it gets assigned a value other than None.

Related

RStudio Error: Unused argument ( by = ...) when fitting gam model, and smoothing seperately for a factor

I am still a beginnner in R. For a project I am trying to fit a gam model on a simple dataset with a timeset and year. I am doing it in R and I keep getting an error message that claims an argument is unused, even though I specify it in the code.
It concerns a dataset which includes a categorical variable of "Year", with only two levels. 2020 and 2022. I want to investigate if there is a peak in the hourly rate of visitors ("H1") in a nature reserve. For each observation period the average time was taken, which is the predictor variable used here ("T"). I want to use a Gam model for this, and have the smoothing applied differently for the two years.
The following is the line of code that I tried to use
`gam1 <- gam(H1~Year+s(T,by=Year),data = d)`
When I try to run this code, I get the following error message
`Error in s(T, by = Year) : unused argument (by = Year)`
I also tried simply getting rid of the "by" argument
`gam1 <- gam(H1~Year+s(T,Year),data = d)`
This allows me to run the code, but when trying to summon the output using summary(gam1), I get
Error in [<-(tmp, snames, 2, value = round(nldf, 1)) : subscript out of bounds
Since I feel like both errors are probably related to the same thing that I'm doing wrong, I decided to combine the question.
Did you load the {mgcv} package or the {gam} package? The latter doesn't have factor by smooths and as such the first error message is what I would expect if you did library("gam") and then tried to fit the model you showed.
To fit the model you showed, you should restart R and try in a clean session:
library("mgcv")
# load you data
# fit model
gam1 <- gam(H1 ~ Year + s(T, by = Year), data = d)
It could well be that you have both {gam} and {mgcv} loaded, in which case whichever you loaded last will be earlier on the function search path. As both packages have functions gam() and s(), R might just be finding the wrong versions (masking), so you might also try
gam1 <- mgcv::gam(H1 ~ Year + mgcv::s(T, by = Year), data = d)
But you would be better off only loading {mgcv} if you wan factor by smooths.
#Gavin Simpson
I did have both loaded, and I tried just using mgcv as you suggested. However, then I get the following error.
Error in names(dat) <- object$term :
'names' attribute [1] must be the same length as the vector [0]
I am assuming this is simply because it's not actually trying to use the "gam" function, but rather it attempts to name something gam1. So I would assume I actually need the package of 'gam' before I could do this.
The second line of code also doesn't work. I get the following error
Error in model.frame.default(formula = H1 ~ Year + mgcv::s(T, by = Year), :
invalid type (list) for variable 'mgcv::s(T, by = Year)'
This happens no matter the order I download the two packages in. And if I don't download 'gam', I get the error as described above.

ImageJ batch processing - opening a series of images containing a specific name and doing stuff on them

I have 25K tif files (please don't ask why) that I want to organize into stacks on image J. Basically for each region of interest (ROI), there are 50 images which breaks down into 25 z-planes for two channels. I want everything in a single stack. And I'd like to batch process the whole folder without opening 50 images 500 times at a time. I've attached a picture of what the file names look like:
Folder organization
r01c01f01p01-ch1.tif - the first 10 characters are unique ID to each ROI, then plane number (p01) then channel - ch1 or ch2, then file extension
Here's what I have so far (which I cobbled together based on other macros so this may not make sense...).This is using the ImageJ macros language.
//Processing loop to process each file in the folder.
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
if (endsWith(list[i], ".tif")) { // skip the subfolder (I create a subfolder earlier in the macros)
print("-- Processing file: " + list[i] + " --");
open(dir+list[i]);
imageTitle= getTitle();
newTitle = substring(imageTitle, 0, lengthOf(imageTitle)-10); // r01c01f01p, cutting off plane number and then the rest to just get the ROI ID
//This is where I'm stuck:
// find all files containing newTitle and open them (which would be 50 at a time), then run the following macros on them
run("Images to Stack", "name=Ch1 title=[] use");
run("Duplicate...", "title=Ch2 duplicate");
selectWindow("Ch1");
run("Slice Remover", "first=1 last=50 increment=2");
selectWindow("Ch2");
run("Slice Remover", "first=2 last=50 increment=2");
run("Merge Channels...", "c1=Ch1 c2=Ch2 create");
saveAs("tiff", dirNew + newTitle + "_Stack.tif");
//Close(All)?
}
}
print("-- Done --");
showStatus("Finished.");
setBatchMode(false); // Exit batch mode
run("Collect Garbage");
Thank you!
You could do something like:
for (plane=1; plane<51; plane++) {
open(newTitle+plane+"-ch1.tif");
open(newTitle+place+"-ch2.tif");
}
Which would take care of the opening. I would be inclined to have a loop prior to this which would collate the number of unique "newTitle"'s, as your current setup would end up doing something like opening the first item, assembling the combined TIF, and then repeat the process 25K times if I understand it correctly.
Given that you know the number of unique "r01c01f01p" values, in principle you could do a set of stacked loops akin to:
newTitleArray = newArray();
for (r=1; r<50; r++) {
titleBit = "r0" + toString(r);
for (c=1; c<501; c++) {
titleBit = titleBit + "f0"...
Alternatively, you could set up a loop where you check for unique "r01c01f01p" values and add them to an array. In any case, you'd replace the for "list" loop with the for "newTitleArray" loop, and then continue onto the opener I listed above, instead of your existing one.
If I am understanding correctly, it seems like you might do well to stack by channel first, then merge the two. I am not 100% sure, but I think you could potentially use a macro I have already created to do that. It was originally meant to batch process terabytes of 5D data, so it should be very comfortable handling your volume of images. It is not exactly what you are looking for, but should be super easy to modify (I went a little overboard with the commenting in the code), and I think the only thing it does that you might rather it not is produce max projects from the inputs. I'll throw a link here and look for your reply. If it's of interest, let me know and we can work to make it suit your needs together :-) Otherwise, if you could provide a little more detail about where you're getting stuck and/or where I may have misunderstood, I will do my very best to help!
https://github.com/evanjkiely/FIJIMacros

How to use Bioproject ID, for example, PRJNA12997, in biopython?

I have an Excel file in which are given more then 2000 organisms, where each one of them has a Bioproject ID associated (like PRJNA12997). The idea is to use these IDs to get the sequence for a later multiple alignment with other five sequences that I have in a text file.
Can anyone help me understand how I can do this using biopython? At least the part with the bioproject ID.
You can first get the info using Bio.Entrez:
from Bio import Entrez
Entrez.email = "Your.Name.Here#example.org"
# This call to efetch fails sometimes with a 400 error.
handle = Entrez.efetch(db="bioproject", id="PRJNA12997")
I've been trying, and Entrez.read(handle) doesn't seems to work. But if you do record_xml = handle.read() you'll get the XML entry for this record. In this XML you can get the ID for the organism, in this case 12997.
handle = Entrez.esearch(db="nuccore", term="12997[BioProject]")
search_results = Entrez.read(handle)
Now you can efecth from your search results. At this point you should use Biopython to parse whatever you will get in the efetch step, playing with the rettype http://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/
for result in search_results["IdList"]:
entry = Entrez.efetch(db="nuccore", id=result, rettype="fasta")
this_seq_in_fasta = entry.read()

pseudo randomization in loop PsychoPy

I know other people have asked similar questions in past but I am still stuck on how to solve the problem and was hoping someone could offer some help. Using PsychoPy, I would like to present different images, specifically 16 emotional trials, 16 neutral trials and 16 face trials. I would like to pseudo randomize the loop such that there would not be more than 2 consecutive emotional trials. I created the experiment in Builder but compiled a script after reading through previous posts on pseudo randomization.
I have read the previous posts that suggest creating randomized excel files and using those, but considering how many trials I have, I think that would be too many and was hoping for some help with coding. I have tried to implement and tweak some of the code that has been posted for my experiment, but to no avail.
Does anyone have any advice for my situation?
Thank you,
Rae
Here's an approach that will always converge very quickly, given that you have 16 of each type and only reject runs of more than two emotion trials. #brittUWaterloo's suggestion to generate trials offline is very good--this what I do myself typically. (I like to have a small number of random orders, do them forward for some subjects and backwards for others, and prescreen them to make sure there are no weird or unintended juxtapositions.) But the algorithm below is certainly safe enough to do within an experiment if you prefer.
This first example assumes that you can represent a given trial using a string, such as 'e' for an emotion trial, 'n' neutral, 'f' face. This would work with 'emo', 'neut', 'face' as well, not just single letters, just change eee to emoemoemo in the code:
import random
trials = ['e'] * 16 + ['n'] * 16 + ['f'] * 16
while 'eee' in ''.join(trials):
random.shuffle(trials)
print trials
Here's a more general way of doing it, where the trial codes are not restricted to be strings (although they are strings here for illustration):
import random
def run_of_3(trials, obj):
# detect if there's a run of at least 3 objects 'obj'
for i in range(2, len(trials)):
if trials[i-2: i+1] == [obj] * 3:
return True
return False
tr = ['e'] * 16 + ['n'] * 16 + ['f'] * 16
while run_of_3(tr, 'e'):
random.shuffle(tr)
print tr
Edit: To create a PsychoPy-style conditions file from the trial list, just write the values into a file like this:
with open('emo_neu_face.csv', 'wb') as f:
f.write('stim\n') # this is a 'header' row
f.write('\n'.join(tr)) # these are the values
Then you can use that as a conditions file in a Builder loop in the regular way. You could also open this in Excel, and so on.
This is not quite right, but hopefully will give you some ideas. I think you could occassionally get caught in an infinite cycle in the elif statement if the last three items ended up the same, but you could add some sort of a counter there. In any case this shows a strategy you could adapt. Rather than put this in the experimental code, I would generate the trial sequence separately at the command line, and then save a successful output as a list in the experimental code to show to all participants, and know things wouldn't crash during an actual run.
import random as r
#making some dummy data
abc = ['f']*10 + ['e']*10 + ['d']*10
def f (l1,l2):
#just looking at the output to see how it works; can delete
print "l1 = " + str(l1)
print l2
if not l2:
#checks if second list is empty, if so, we are done
out = list(l1)
elif (l1[-1] == l1[-2] and l1[-1] == l2[0]):
#shuffling changes list in place, have to copy it to use it
r.shuffle(l2)
t = list(l2)
f (l1,t)
else:
print "i am here"
l1.append(l2.pop(0))
f(l1,l2)
return l1
You would then run it with something like newlist = f(abc[0:2],abc[2:-1])

Maximo scripting cannot load second MboSet

I've a script with an object launchpoint on INVOICELINE.
For the mbo I want to get all INVOICELINES with the same PONUM as the current MBO (since they could be in other then the current mbo's invoice)
In the script I find the PO like so: (to test for status)
from psdi.server import MXServer
from psdi.mbo import Mbo
from psdi.mbo import MboConstants
from psdi.security import UserInfo
from psdi.server import MXServer
myMXServer = MXServer.getMXServer()
userInfo = mbo.getThisMboSet().getUserInfo()
# find the PO
poSet = myMXServer.getMboSet("PO", userInfo)
poSetWhere = "ponum='" + mbo.getString("PONUM") + "' and siteid='" + mbo.getString("POSITEID") + "' and status not in " + poNoUpdate
poSet.setWhere(poSetWhere)
poMbo = poSet.getMbo(0)
which works great.
then later I do the very same for the set of invoicelines:
ilSet = myMXServer.getMboSet("INVOICELINE", userInfo)
ilSetWhere = "ponum='" + mbo.getString("PONUM") + "' and positeid='" + mbo.getString("POSITEID") + "'"
ilSet.setWhere(ilSetWhere)
ilMbo = ilSet.moveFirst()
while ilMbo is not None:
...
which results in a error on the setWhere line. Curiously, logging (which I removed for readability) indicates that ilSet contains all invoicelines records after the getMboSet (as expected), the ilSetWhere has a valid query that you can copy-paste in SQL Developer.
Does Maximo need some index or so before it can execute this setWhere?
Here is the logging result for the two setWhere strings:
ponum='4140006682' and siteid='mysite' and status not in ('CLOSED','CAN','GESLTN','ANN')
and
ponum='4140006682' and positeid='mysite'
The error I get is a generic BMXAA7837E java.lang.NullPointerException in script at line... (the line refers to the line with the ilSet.setWhere(ilSetWhere) expression. I'm out of ideas how to fix this and have no clue how to work around it.
Now we have an error to work with!
Maximo effectively insists that an INVOICELINE set has an "owner", which you have not set up in your code example. Think of an owner as a parent set. Specifically, it is the MBOSet used to fetch the current set off of. It doesn't actually have to be related to the current set, but most of the time it will be (and it makes the most sense to fetch sets that way). An owner can be injected into the set after it's fetched (to change it or trick Maximo), but this is rarely good code.
Instead of getting a fresh set (no other ties or possible data caching) from the server in its own transaction, you might be best off getting the invoiceline set off of your current MBO. I don't know your exact use case, but generally you want to do something like this instead of getting a new set like you did. At the least, it will give your new set an "owner". You may even want to make the SQL a "relationship" instead of hard-coding it.
ilSetWhere = "ponum='" + mbo.getString("PONUM") + "' and positeid='" + mbo.getString("POSITEID") + "'"
ilSet = mbo.getMboSet("$TempInvoiceLineRelationship", "INVOICELINE", ilSetWhere)
ilMbo = ilSet.moveFirst()
I'm going from memory for this code, so I don't know if it is exactly correct. That form of "getMboSet" takes three parameters. The first is a relationship name. If Maximo finds that relationship name already "registered" from this starting object, it will ignore the next two parameters and use that relationship to get you that set. If it doesn't find that relationship "registered" it registers it for the scope of this code (so you can re-use it later in this code if you wanted). The second parameter defines what destination object to create the temporary relationship to. The third parameter defines the "where clause" of this temporary relationship.
Original Answer:
What is the error you are getting?
Also, you say you log "ilSet" after the "myMXServer.getMboSet..." line? That is going to cause Maximo to run the query and load the objects into the set at that point (it waits to run the query until it has to). As a result of that, you won't see the effects of your where clause change until you "reset()" the set.