Add codespell support with configuration and fixes

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git,.git-meta,.gitignore,.gitattributes,*.pdf,*.svg,*.css,.codespellrc,*/jsPsych/*
+check-hidden = true
+ignore-regex = ^\s*"image/\S+": ".*
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@8f01853be192eb0f849a5c7d721450e7a467c579  # v2.2

Readme.md

@@ -20,7 +20,7 @@ There you can find full example projects, demos of Psychopy integration, and emp
 
 **Overview of RT-Cloud Components**
 ![](docs/rtcloud_schematic.png )<br>
-- **data_streamer** (runs on machine that recieves/sends DICOMs)
+- **data_streamer** (runs on machine that receives/sends DICOMs)
   - Watches for new DICOM brain images and sends them to whatever machine is analysing the data
   - Can simulate the transfer of DICOMs from the MRI scanner using a precollected folder of DICOMs or via an OpenNeuro dataset (OpenNeuroService)
 - **data_analyser** (runs on machine that analyses data in real-time)

docker/Dockerfile.rttools

@@ -18,7 +18,7 @@ echo 'export FSLDIR PATH' >> ~/.bashrc && \
 echo 'export LD_LIBRARY_PATH=${FSLDIR}/lib:${FSLDIR}/fslpython/lib:${LD_LIBRARY_PATH}' >> ~/.bashrc && \
 echo "## FSL Install Complete ##" && \
 # Remove bulk of FSL (including fsleyes!) leaving only binary analysis functions
-echo "## Removing non-essential FSL utilites! ##" && \
+echo "## Removing non-essential FSL utilities! ##" && \
 source ~/.bashrc && \
 cd $FSLDIR && \
 yes | rm -r config data doc extras fslpython include lib python refdoc src tcl && \

docs/conf.py

@@ -40,7 +40,7 @@
 # 2) AutoAPI uses code parsing instead of code imports, which means there's no
 # need to install the full RT-Cloud conda environment (takes >10m on RTD).
 autoapi_dirs = ['../rtCommon']
-# autoapi_keep_files = True  # Useful for debuggin warnings and errors
+# autoapi_keep_files = True  # Useful for debugging warnings and errors
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/for-developers.md

@@ -95,7 +95,7 @@ The experiment script doesn’t need to change anything to use the 3 ways of int
 **Q:** I’m not sure i understand the difference between “ProjectServer with local services” and “ProjectServer with remote services”. (Especially because earlier in this document you say that if a module is running remotely then you call it a service — so i thought service means “remote”, but here you refer to local vs remote services)
 - **A:** The projectServer and the experiment script always run on the same computer, this is baked into the code that the clientInterface is only allowed to make a localhost connection to the projectServer (for security reasons). So whether the dataInterface is running within the experiment script (case 1) or in the projectServer (case 2) it is still local to the computer that the experiment script is running on, so in that sense the data is local to the script.
 
-**Q:** Even if I am just testing things out (using --test flag) by running two terminals on my local machine, one as projectServer + dataService, the other as subjectService, I still need to have a valid ssl cert? and I cant test out the exporting of text files with dequeueResult via the outputDir flag unless I am using a “remote” subjectservice right?
+**Q:** Even if I am just testing things out (using --test flag) by running two terminals on my local machine, one as projectServer + dataService, the other as subjectService, I still need to have a valid ssl cert? and I can't test out the exporting of text files with dequeueResult via the outputDir flag unless I am using a “remote” subjectservice right?
 - **A:** You don’t need an ssl cert with --test flag, but you must specify --test for each process you start (the subjectInterface as well as projectServer).
 Yes, you need a remote subjectService to test the writing of text files.
 
@@ -107,10 +107,10 @@ Yes, you need a remote subjectService to test the writing of text files.
 
 
 **Q:** What’s the difference between initWatch and initScannerStream?
-- **A:**  initWatch and initScannerStream both accomplish the same thing. We originally had the initWatch/watchFile interface. Then we added a more “streaming” interface with BIDS and the initScannerStream/getImageData is that. So the BIDS interface uses initScannerStream internally, but it can also be used for a Dicom stream. I would say use the initScrannerStream interface and consider the initWatch as deprecated (or for backward compatibility).
+- **A:**  initWatch and initScannerStream both accomplish the same thing. We originally had the initWatch/watchFile interface. Then we added a more “streaming” interface with BIDS and the initScannerStream/getImageData is that. So the BIDS interface uses initScannerStream internally, but it can also be used for a Dicom stream. I would say use the initScannerStream interface and consider the initWatch as deprecated (or for backward compatibility).
 
 **Q:** Can I have the experiment script execute different code dependent on a subject’s button press? if so how would i let the experiment script have access to that information of what/if the subject pressed a button?
-- **A:** There is some support for getResponses, and I made an example in the jsPsych feedback. For PsychoPy the subject responses would need to be queued and returned whenever the experiment script calls getResponse or getAllReponses. So the stubs are there, it just needs to be filled out some.
+- **A:** There is some support for getResponses, and I made an example in the jsPsych feedback. For PsychoPy the subject responses would need to be queued and returned whenever the experiment script calls getResponse or getAllResponses. So the stubs are there, it just needs to be filled out some.
 
 **Q:** How can I can test the VNC Viewer locally? Can I run the DISPLAY=:1 code in the experiment script file?
 - **A:** You can install tigervnc and the websocket conda environment. See instructions [here](https://rt-cloud.readthedocs.io/en/latest/how-to-run.html?highlight=vnc#install-vnc-server-on-the-projectserver-computer).
@@ -119,5 +119,5 @@ The scripts/run-vnc.sh will then start the vnc server and create a websockify wr
 Other Notes from discussion:
 - How can I change the experiment script based on button presses? Answer: currently only implemented in javascript version of subjectinterface via getAllResponses(); not implemented in python subjectinterface yet; probably not good idea to go from control room machine to cloud directly.
 - we also talked about some vnc viewer specifics — needs its own installation, new conda environment, etc
-- also talked about how you cant easily view analyzed data on the control room machine (going from cloud back to the control room to bypass using VNC viewer), or you can depending on your MRI Center’s setup but we want rtcloud to be workable regardless of the setup
+- also talked about how you can't easily view analyzed data on the control room machine (going from cloud back to the control room to bypass using VNC viewer), or you can depending on your MRI Center’s setup but we want rtcloud to be workable regardless of the setup
 you can potentially bypass VNC Viewer by encoding the image you want to look at into a dictionary and sending that through to the presentation laptop, but at that point its probably not worth it compared to the initial setup cost of doing VNC viewer route

docs/subject-feedback.md

@@ -11,7 +11,7 @@ The source code components of jsPsych live in the `web/` directory. File `web/js
 
 2. Connect a web browser to the main page
     - http://localhost:8888/
-    - Enter 'test' for both the usnername and password since we are running it in unsecure test mode.
+    - Enter 'test' for both the username and password since we are running it in insecure test mode.
 
 3. Connect a web browser to the jsPsych feedback page
     - http://localhost:8888/jspsych

docs/tutorials/bids_tutorial.ipynb

@@ -261,7 +261,7 @@
     "events = archive.getEvents(subject='01', \n",
     "                           task='languageproduction', run=1)\n",
     "\n",
-    "# All event files can be retrieved when specifiying no entities\n",
+    "# All event files can be retrieved when specifying no entities\n",
     "events = archive.getEvents()\n",
     "\n",
     "# Event files are returned as BIDSDataFile objects\n",

docs/using-bids-data.md

@@ -28,7 +28,7 @@ https://bids-specification.readthedocs.io/en/stable/, a few key details are as
 follows:
 
 1.  **Brain imaging data is stored in the Neuroimaging Informatics
-    Technology Initative (NIfTI) format.** NIfTI is a binary file format
+    Technology Initiative (NIfTI) format.** NIfTI is a binary file format
     that starts with a header holding basic information about the brain
     data contained in the file. The header is followed by the raw brain
     data. A NIfTI volume's data typically has 4 dimensions, *x, y, z*

environment-synthetic-data.yml

@@ -3,6 +3,6 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - brainiak::brainiak  # specifing the channel
+  - brainiak::brainiak  # specifying the channel
   - nomkl
   - scikit-learn

projects/dicomBidsStream/dicomBidsStream.py

@@ -15,7 +15,7 @@
 
 Finally, this script is called from the projectInterface which has a web interface
 and accepts commands to 'start' or 'stop' a run. When the 'start' button is
-pressed it will run this scirpt passing in whatever conifgurations have been
+pressed it will run this script passing in whatever configurations have been
 set in the web page as a configuration file. Note that projectInterface is
 started from the script 'run-projectInterface.sh'.
 
@@ -141,7 +141,7 @@ def doRuns(cfg, clientInterfaces):
                 accidentally grab a dicom before it's fully acquired)
     """
     if verbose:
-        print("• initalize a watch for the dicoms using 'initWatch'")
+        print("• initialize a watch for the dicoms using 'initWatch'")
     entities = {'subject': cfg.subjectName, 'task': 'test', 'run': runNum}
     streamId = bidsInterface.initDicomBidsStream(cfg.dicomDir, dicomScanNamePattern, 
                                                  cfg.minExpectedDicomSize, **entities)
@@ -286,7 +286,7 @@ def main(argv=None):
     argParser.add_argument('--scans', '-s', default=None, type=str,
                            help='Comma separated list of scan number')
     argParser.add_argument('--yesToPrompts', '-y', default=False, action='store_true',
-                           help='automatically answer tyes to any prompts')
+                           help='automatically answer yes to any prompts')
 
     # Some additional parameters only used for this sample project
     argParser.add_argument('--noVerbose', '-nv', default=False, action='store_true',

projects/openNeuroClient/openNeuroClient.py

@@ -72,7 +72,7 @@ def main(argv=None):
     argParser.add_argument('--runs', '-r', default=None, type=str,
                            help='Comma separated list of run numbers')
     argParser.add_argument('--yesToPrompts', '-y', default=False, action='store_true',
-                           help='automatically answer tyes to any prompts')
+                           help='automatically answer yes to any prompts')
     argParser.add_argument('--archive', '-a', default=False, action='store_true',
                            help='Create a Bids Archive from the incoming Bids Incrementals.')
     args = argParser.parse_args(argv)

projects/sample/README.md

@@ -72,6 +72,6 @@ All of the functions we use within the real-time fMRI cloud framework live in th
 - **`fileClient` script**
     - The functions enable you to interact with files, from starting a lookout (or watch) for a specific type of file to displaying all of the allowed file types.
 - **`projectUtils` script**
-    - The functions here allow you to interface between the cloud and the consol computer. For instance, if you want to download files from the cloud there's a function to help you do that here!
+    - The functions here allow you to interface between the cloud and the console computer. For instance, if you want to download files from the cloud there's a function to help you do that here!
 - **`imageHandling` script**
     - The purpose of these functions is to help you (1) transfer dicom files back and forth from the cloud and (2) convert the dicom files to nifti files, which is a file format that is better for data analyses.

projects/sample/finalize.py

@@ -3,7 +3,7 @@
 initialize.py (Last Updated: 01/26/2021)
 
 The purpose of this script is to finalize the rt-cloud session. Specifically,
-here we want to dowload any important files from the cloud back to the stimulus
+here we want to download any important files from the cloud back to the stimulus
 computer and maybe even delete files from the cloud that we don't want to 
 stay there (maybe for privacy purposes).
 

projects/sample/initialize.py

@@ -13,7 +13,7 @@
     "-----------------------------------------------------------------------------\n"
     "The purpose of this script is to show you the ways in which you can utilize\n"
     "an initialization function. You will notice some comments printed on the\n"
-    "html browser, but if you want more details please look at initalize.py.\n"
+    "html browser, but if you want more details please look at initialize.py.\n"
     "-----------------------------------------------------------------------------")
 
 import os
@@ -141,9 +141,9 @@ def main(argv=None):
 
 if __name__ == "__main__":
     """
-    If 'initalize.py' is invoked as a program, then actually go through all of the 
+    If 'initialize.py' is invoked as a program, then actually go through all of the 
     portions of this script. This statement is not satisfied if functions are called 
-    from another script using "from initalize.py import FUNCTION"
+    from another script using "from initialize.py import FUNCTION"
     """
     main()
     sys.exit(0)

projects/sample/sample.py

@@ -13,7 +13,7 @@
 
 Finally, this script is called from the projectInterface which has a web interface
 and accepts commands to 'start' or 'stop' a run. When the 'start' button is
-pressed it will run this scirpt passing in whatever conifgurations have been
+pressed it will run this script passing in whatever configurations have been
 set in the web page as a configuration file. Note that projectInterface is
 started from the script 'run-projectInterface.sh'.
 
@@ -82,7 +82,7 @@ def doRuns(cfg, dataInterface, subjInterface, webInterface):
 
     INPUT:
         [1] cfg - configuration file with important variables)
-        [2] dataInterface - this will allow this script runnin in the cloud to access
+        [2] dataInterface - this will allow this script running in the cloud to access
                 files from the stimulus computer, which receives dicom files directly
                 from the MRI Scanner console
         [3] subjInterface - this allows sending feedback (e.g. classification results)
@@ -165,7 +165,7 @@ def doRuns(cfg, dataInterface, subjInterface, webInterface):
                     accidentally grab a dicom before it's fully acquired)
         """
         if verbose:
-            print("• initalize a watch for the dicoms using 'initWatch'")
+            print("• initialize a watch for the dicoms using 'initWatch'")
         dataInterface.initWatch(cfg.dicomDir, dicomScanNamePattern, 
                                 cfg.minExpectedDicomSize, demoStep=demoTimeDelay)
 
@@ -408,7 +408,7 @@ def main(argv=None):
     argParser.add_argument('--scans', '-s', default=None, type=str,
                            help='Comma separated list of scan number')
     argParser.add_argument('--yesToPrompts', '-y', default=False, action='store_true',
-                           help='automatically answer tyes to any prompts')
+                           help='automatically answer yes to any prompts')
 
     # Some additional parameters only used for this sample project
     argParser.add_argument('--useInitWatch', '-w', default=False, action='store_true',

rtCommon/bidsArchive.py

@@ -790,7 +790,7 @@ def appendBidsRun(self, run: BidsRun) -> None:
         Append a BIDS Run to this archive.
 
         Args:
-            run: Run to append to the archvie.
+            run: Run to append to the archive.
 
         Examples:
             >>> archive1 = BidsArchive('/tmp/dataset1')

rtCommon/bidsCommon.py

@@ -30,7 +30,7 @@
                         "Authors": ["The RT-Cloud Authors",
                                     "The Dataset Author"]}
 
-# Deafult readme text for RT-Cloud
+# Default readme text for RT-Cloud
 DEFAULT_README = "Generated BIDS-Incremental Dataset from RT-Cloud"
 
 # Required columns for the BIDS events files
@@ -81,7 +81,7 @@ class BidsFileExtension(Enum):
     EVENTS = '.tsv'
 
 
-# BIDS Entitiy information dict
+# BIDS Entity information dict
 class BidsEntityKeys(Enum):
     ENTITY = "entity"
     FORMAT = "format"

rtCommon/bidsIncremental.py

@@ -236,7 +236,7 @@ def __setstate__(self, state):
 
     def _preprocessMetadata(self, imageMetadata: dict) -> dict:
         """
-        Pre-process metadata to extract any additonal metadata that might be
+        Pre-process metadata to extract any additional metadata that might be
         embedded in the provided metadata, like ProtocolName, and ensure that
         certain metadata values (e.g., RepetitionTime) are within
         BIDS-specified ranges.
@@ -496,7 +496,7 @@ def getImageData(self) -> np.ndarray:
     BEGIN BIDS-I ARCHIVE EMULTATION API
 
     A BIDS-I is meant to emulate a valid BIDS archive. Thus, an API is included
-    that enables generating paths and filenames that would corresopnd to this
+    that enables generating paths and filenames that would correspond to this
     BIDS-I's data if it were actually in an on-disk archive.
 
     """

rtCommon/bidsInterface.py

@@ -61,7 +61,7 @@ def __init__(self, dataRemote=False, allowedDirs=[], scannerClockSkew=0):
     def initDicomBidsStream(self, dicomDir, dicomFilePattern, dicomMinSize,
                             anonymize=True, **entities) -> int:
         """
-        Intialize a data stream that watches a directory for DICOM files to be written that
+        Initialize a data stream that watches a directory for DICOM files to be written that
         match the given file pattern. When a DICOM is written it will be converted to a BIDS
         incremental and returned.
 
@@ -176,7 +176,7 @@ def getClockSkew(self, callerClockTime: float, roundTripTime: float) -> float:
         # Adjust the caller's clock forward by 1/2 round trip time
         callerClockAdjToNow = callerClockTime + roundTripTime / 2.0
         now = time.time()
-        # calcluate the time this server's clock is ahead of the caller's clock
+        # calculate the time this server's clock is ahead of the caller's clock
         skew = now - callerClockAdjToNow
         # add the time skew from this server to the scanner clock
         totalSkew = skew + self.scannerClockSkew
@@ -201,7 +201,7 @@ def __init__(self, allowedDirs=[]):
     def initStream(self, dicomDir, dicomFilePattern, dicomMinSize,
                    anonymize=True, **entities):
         """
-        Intialize a new DicomToBids stream, watches for Dicoms and streams as BIDS
+        Initialize a new DicomToBids stream, watches for Dicoms and streams as BIDS
 
         Args:
             dicomDir: The directory where the scanner will write new DICOM files