Fixed problems processing Mulit-Echo images

Dockerfile

@@ -1,6 +1,7 @@
 #flywheel/fmriprep
 
-FROM python:3.7
+#FROM python:3.7
+FROM python:3.10
 MAINTAINER Tinashe Tapera <[email protected]>
 
 # Make directory for flywheel spec (v0)
@@ -13,14 +14,15 @@ ENTRYPOINT ["/flywheel/v0/fw_heudiconv_run.py"]
 
 # Copy over python scripts that generate the BIDS hierarchy
 RUN apt-get -y update && apt-get install -y curl
-RUN curl -sL https://deb.nodesource.com/setup_10.x | bash - &&\
+#RUN curl -sL https://deb.nodesource.com/setup_10.x | bash - &&\
+RUN curl -fsSL https://deb.nodesource.com/setup_21.x | bash - &&\
     apt-get -y install nodejs &&\
     ln -s /usr/bin/nodejs /usr/local/bin/node
 RUN curl -L https://www.npmjs.com/install.sh | sh
 RUN npm install -g bids-validator
 RUN python3 -m pip install --upgrade pip
 RUN pip install --no-cache nipype pathvalidate
-RUN pip install --no-cache flywheel-sdk~=14.6.5
+RUN pip install --no-cache flywheel-sdk
 
 COPY . /src
 

docs/source/environment.yml

@@ -15,7 +15,6 @@ dependencies:
 - sphinx_rtd_theme
 - mock
 - future
-- nibabel
 - statsmodels
 - xvfbwrapper
 - configparser

fw_heudiconv/backend_funcs/query.py

@@ -4,7 +4,6 @@
 import warnings
 with warnings.catch_warnings():
     warnings.filterwarnings("ignore", category=UserWarning)
-    from nibabel.nicom.dicomwrappers import wrapper_from_data
 
 
 CONVERTABLE_TYPES = ("bvec", "bval", "nifti")
@@ -63,15 +62,30 @@ def acquisition_to_heudiconv(client, acq, context):
         zip_info = None
         dcm_info = {}
     # Make it a nicom wrapper to handle all sorts of different dicom styles
-    mw = wrapper_from_data(dcm_info)
+    #mw = wrapper_from_data(dcm_info)
+    #log.info("mw.image_shape = '{}'".format(mw.image_shape))
     num_dicoms = len(zip_info.members) if zip_info else -1
-    image_shape = mw.image_shape
-    if image_shape is None:
-        image_shape = (-1, -1, -1, -1)
-    else:
-        image_shape = mw.image_shape + (num_dicoms,)
-        while len(image_shape) < 4:
-            image_shape = image_shape + (-1,)
+    #image_shape = mw.image_shape
+    #if image_shape is None:
+    #    image_shape = (-1, -1, -1, -1)
+    #else:
+        #image_shape = mw.image_shape + (num_dicoms,)
+    #    while len(image_shape) < 4:
+    #        image_shape = image_shape + (-1,)
+
+    Rows = -1
+    if "Rows" in dcm_info:
+        Rows = dcm_info["Rows"]
+
+    Columns = -1 
+    if ("Columns" in dcm_info):
+        Columns = dcm_info["Columns"]
+
+    image_shape = (-1, -1, -1, -1)
+    if (Rows > 0 and Columns > 0):
+       image_shape = (Rows, Columns, num_dicoms, -1)
+
+    log.info("{}: Image Shape = '{}', num_dicoms = '{}'".format(acq.label,image_shape,num_dicoms))
 
     for fileobj in acq.files:
         log.debug('filename: %s', fileobj.name)
@@ -80,7 +94,7 @@ def acquisition_to_heudiconv(client, acq, context):
         info = fileobj.info
 
         # Make it a nicom wrapper to handle all sorts of different dicom styles
-        mw = wrapper_from_data(info)
+        #mw = wrapper_from_data(info)
 
         log.debug('uid: %s', info.get("SeriesInstanceUID"))
         to_convert.append(SeqInfo(

fw_heudiconv_run.py

@@ -15,6 +15,9 @@
 
 # start up inputs
 invocation = json.loads(open('config.json').read())
+
+logger.info(json.dumps(invoication, indent=2))
+
 config = invocation['config']
 inputs = invocation['inputs']
 destination = invocation['destination']

manifest.json

@@ -1,43 +1,63 @@
 {
-	"name": "fw-heudiconv",
-	"label": "Flywheel HeuDiConv",
-	"description": "HeuDiConv-style BIDS curation on Flywheel. Flywheel HeuDiConv (or fw-heudiconv, pronounced /fwuː di kɑː n(v)/) is a Python-based toolkit that leverages the flexibility and comprehensiveness of HeuDiConv to curate neuroimaging data on Flywheel into a BIDS-valid format.",
-	"version": "0.2.15_0.4.3",
-	"inputs": {
-		"api_key": {
-			"base": "api-key"
-		},
-		"heuristic": {
-			"base": "file",
-			"description": "Python file implementing a heudiconv heuristic",
-			"optional": true
-		}
-	},
-	"config": {
-		"action": {
-			"default": "Curate",
-			"description": "Curate: Apply heuristic to project. Export: Create zip of BIDS tree. Tabulate: Create a table of sequence information in a project. Clear: Clear BIDS data from project. Reproin Check: Apply the reproin heuristic to a list of reproin names to check for validity. Meta: Autogenerate BIDS metadata for project.",
-			"type": "string",
-			"enum": ["Curate", "Export", "Tabulate", "Clear", "Reproin", "Validate"]
-		},
-		"dry_run": {
-			"default": true,
-			"description": "Run without applying changes",
-			"type": "boolean"
-		}
-	},
-	"command": "./fw_heudiconv_run.py",
-	"author": "Tinashe Michael Tapera",
-	"maintainer": "Tinashe Michael Tapera",
-	"cite": "",
-	"license": "Other",
-	"source": "",
-	"url": "https://github.com/PennBBL/fw-heudiconv",
-	"custom": {
-		"gear-builder": {
-			"category": "analysis",
-			"image": "pennbbl/fw-heudiconv:0.2.15_0.4.3"
-		},
-		"flywheel":{"suite": "PennBBL"}
-	}
-}
+    "name": "dev-fw-heudiconv",
+    "label": "Dev Flywheel HeuDiConv",
+    "description": "HeuDiConv-style BIDS curation on Flywheel. Flywheel HeuDiConv (or fw-heudiconv, pronounced /fwu\u02d0 di k\u0251\u02d0 n(v)/) is a Python-based toolkit that leverages the flexibility and comprehensiveness of HeuDiConv to curate neuroimaging data on Flywheel into a BIDS-valid format.",
+    "version": "0.2.15_1.0.1-dev-001",
+    "inputs": {
+        "api_key": {
+            "base": "api-key"
+        },
+        "heuristic": {
+            "base": "file",
+            "description": "Python file implementing a heudiconv heuristic",
+            "optional": true
+        }
+    },
+    "config": {
+        "action": {
+            "default": "Curate",
+            "description": "Curate: Apply heuristic to project. Export: Create zip of BIDS tree. Tabulate: Create a table of sequence information in a project. Clear: Clear BIDS data from project. Reproin Check: Apply the reproin heuristic to a list of reproin names to check for validity. Meta: Autogenerate BIDS metadata for project.",
+            "type": "string",
+            "enum": [
+                "Curate",
+                "Export",
+                "Tabulate",
+                "Clear",
+                "Reproin",
+                "Validate"
+            ]
+        },
+        "dry_run": {
+            "default": true,
+            "description": "Run without applying changes",
+            "type": "boolean"
+        }
+    },
+    "command": "./fw_heudiconv_run.py",
+    "author": "Tinashe Michael Tapera",
+    "maintainer": "Tinashe Michael Tapera",
+    "cite": "",
+    "license": "Other",
+    "source": "",
+    "url": "https://github.com/PennBBL/fw-heudiconv",
+    "custom": {
+        "gear-builder": {
+            "category": "analysis",
+            "image": "pennbbl/fw-heudiconv:0.2.15_1.0.1-dev-001"
+        },
+        "flywheel": {
+            "suite": "PennBBL"
+        }
+    },
+    "environment": {
+        "PATH": "/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
+        "LANG": "C.UTF-8",
+        "GPG_KEY": "A035C8C19219BA821ECEA86B64E628F8D684696D",
+        "PYTHON_VERSION": "3.10.14",
+        "PYTHON_PIP_VERSION": "23.0.1",
+        "PYTHON_SETUPTOOLS_VERSION": "65.5.1",
+        "PYTHON_GET_PIP_URL": "https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py",
+        "PYTHON_GET_PIP_SHA256": "dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab9",
+        "FLYWHEEL": "/flywheel/v0"
+    }
+}

release.sh

@@ -29,11 +29,11 @@ fi
 echo Uploading to pip...
 
 python setup.py sdist
-<<<<<<< HEAD
+#<<<<<<< HEAD
 twine upload dist/* --skip-existing
-=======
-twine upload --skip-existing dist/*
->>>>>>> 451d0170cd190ca6cceb86def6dc51bc45a73802
+#=======
+#twine upload --skip-existing dist/*
+#>>>>>>> 451d0170cd190ca6cceb86def6dc51bc45a73802
 
 echo Uploading gear...
 

requirements.txt

@@ -1,11 +1,10 @@
-flywheel-sdk ~= 14.6.5
+flywheel-sdk
 pandas
 bids-validator
 validators
 sphinx-argparse
 commonmark
 pathvalidate
 pytest
-nibabel
 pytest-cov
 heudiconv

setup.cfg

@@ -26,9 +26,8 @@ classifiers =
 
 [options]
 install_requires =
-    flywheel-sdk ~= 14.6.5
+    flywheel-sdk ~= 18.1.1
     bids-validator
-    nibabel >=3.0.0
     indexed_gzip >=0.8.8
     nilearn !=0.5.0, !=0.5.1
     nipype >=1.3.1
@@ -47,7 +46,6 @@ install_requires =
     scikit-learn >=0.20.2
     scikit-image
     statsmodels
-    nibabel
     heudiconv
 test_requires =
     coverage

setup.py

@@ -16,14 +16,13 @@
     url="https://github.com/PennBBL/fw_heudiconv",
     packages=setuptools.find_packages(),
     install_requires=[
-        "flywheel-sdk~=14.6.5",
+        "flywheel-sdk~=18.1.1",
         "pandas",
         "bids-validator",
         "validators",
         "pathvalidate",
         "pytest",
         "pytest-cov",
-        "nibabel",
         "heudiconv"
     ],
     classifiers=[