Merge pull request #181 from bbfrederick/refinedelay

Refinedelay

Dockerfile

@@ -47,20 +47,29 @@ RUN ldconfig
 # clean up
 RUN pip cache purge
 
-# switch to the rapidtide user
-RUN useradd -m -s /bin/bash -G users rapidtide
-RUN chown -R rapidtide /src/rapidtide
-WORKDIR /home/rapidtide
+# Create a shared $HOME directory
+ENV USER=rapidtide
+RUN useradd \
+    --create-home \
+    --shell /bin/bash \
+    --groups users \
+    --home /home/$USER \
+    $USER
+RUN chown -R $USER /src/$USER
+WORKDIR /home/$USER
 ENV HOME="/home/rapidtide"
+
 RUN /opt/miniforge3/bin/mamba init
 RUN echo "mamba activate science" >> /home/rapidtide/.bashrc
 RUN echo "/opt/miniforge3/bin/mamba activate science" >> /home/rapidtide/.bashrc
+
+# switch to the rapidtide user
 USER rapidtide
 
 # set up variable for non-interactive shell
 ENV PATH=/opt/miniforge3/envs/science/bin:/opt/miniforge3/condabin:.:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 
-ENV IS_DOCKER_8395080871=1
+ENV IN_DOCKER_CONTAINER=1
 
 WORKDIR /tmp/
 ENTRYPOINT ["/cloud/mount-and-run"]

rapidtide/util.py

@@ -453,7 +453,7 @@ def version():
 
     """
     try:
-        dummy = os.environ["IS_DOCKER_8395080871"]
+        dummy = os.environ["IN_DOCKER_CONTAINER"]
     except KeyError:
         isdocker = False
     else:

rapidtide/workflows/happy.py

@@ -80,7 +80,7 @@ def happy_main(argparsingfunc):
 
     # if we are running in a Docker container, make sure we enforce memory limits properly
     try:
-        testval = os.environ["IS_DOCKER_8395080871"]
+        testval = os.environ["IN_DOCKER_CONTAINER"]
     except KeyError:
         args.runningindocker = False
     else:

rapidtide/workflows/rapidtide.py

@@ -268,7 +268,7 @@ def rapidtide_main(argparsingfunc):
         print("turning on garbage collection")
 
     # if we are running in a Docker container, make sure we enforce memory limits properly
-    if "IS_DOCKER_8395080871" in os.environ:
+    if "IN_DOCKER_CONTAINER" in os.environ:
         optiondict["runningindocker"] = True
         optiondict["dockermemfree"], optiondict["dockermemswap"] = tide_util.findavailablemem()
         if optiondict["dockermemfix"]:
@@ -3339,6 +3339,28 @@ def rapidtide_main(argparsingfunc):
             debug=optiondict["focaldebug"],
         )
 
+        if optiondict["glmderivs"] == 1:
+            # special case - calculate the ratio of derivative to raw regressor
+            glmderivratio = np.nan_to_num(fitcoeff[:, 1] / fitcoeff[:, 0])
+            ratiolist = np.linspace(-10.0, 10.0, 21, endpoint=True)
+            """outtcs = np.zeros((len(ratiolist), regressorset.shape[]), dtype=rt_floattype)
+            colnames = []
+            for ratioidx in range(outtcs.shape[0]):
+                outtcs[ratioidx, :] = tide_math.stdnormalize(
+                    regressorset[0, :] + ratiolist[ratioidx] * regressorset[1, :]
+                )
+                colnames.append(str(ratiolist[ratioidx]))
+            tide_io.writebidstsv(
+                f"{outputname}_desc-glmratio_timeseries",
+                outtcs,
+                oversampfreq,
+                columns=["filteredRMS", "linearfit"],
+                extraheaderinfo={
+                    "Description": "Filtered RMS amplitude of the probe regressor, and a linear fit"
+                },
+                append=False,
+            )"""
+
         # calculate the final bandlimited mean normalized variance
         finalvariance = tide_math.imagevariance(filtereddata, theprefilter, 1.0 / fmritr)
         divlocs = np.where(finalvariance > 0.0)
@@ -3502,6 +3524,10 @@ def rapidtide_main(argparsingfunc):
             (coherencepeakval, "coherencepeakval", "map", None, "Coherence peak value"),
             (coherencepeakfreq, "coherencepeakfreq", "map", None, "Coherence peak frequency"),
         ]
+    if optiondict["glmderivs"] == 1:
+        savelist += [
+            (glmderivratio, "glmderivratio", "map", None, "GLM derivative ratio"),
+        ]
     tide_io.savemaplist(
         outputname,
         savelist,