adding index map computation

biswebpython/modules/PythonModuleList.txt

@@ -50,3 +50,4 @@ eigenvectorDenoiseImage
 extractImagePatches
 initializeCalciumStudy
 dualImageRegression
+computeImageIndexMap

biswebpython/modules/computeImageIndexMap.py

@@ -0,0 +1,65 @@
+# LICENSE
+# 
+# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
+# 
+# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
+# 
+# - you may not use this software except in compliance with the License.
+# - You may obtain a copy of the License at [http://www.apache.org/licenses/LICENSE-2.0](http://www.apache.org/licenses/LICENSE-2.0)
+# 
+# __Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.__
+# 
+# ENDLICENSE
+
+import biswebpython.core.bis_basemodule as bis_basemodule
+import biswebpython.core.bis_baseutils as bis_baseutils
+import biswebpython.core.bis_objects as bis_objects
+import numpy as np;
+
+class computeImageIndexMAP(bis_basemodule.baseModule):
+
+    def __init__(self):
+        super().__init__();
+        self.name='computeImageIndexMap';
+
+    def createDescription(self):
+
+        return {
+            "name": "compute Image Index Map for sparse Matrix distance computations",
+            "description": "Given an  objectmap compute the image index map (voxels > 0 indexed)",
+            "author": "Xenios Papademetris and Xilin Shen",
+            "version": "1.0",
+                {
+                    "type": "image",
+                    "name": "Objectmap Image",
+                    "description": "The objectmap/mask image",
+                    "varname": "input",
+                    "shortname" : "i",
+                    "required": True,
+                },
+            ],
+            "outputs": bis_baseutils.getImageToImageOutputs('The indexmap image'),
+            "params" : [ 
+                bis_baseutils.getDebugParam()
+            ],
+        }
+
+
+    def directInvokeAlgorithm(self,vals):
+        print('oooo invoking: computeImageIndexMap with vals', vals);
+
+        self.outputs['output']=bis_baseutils.getDynamicLibraryWrapper().computeImageIndexMapWASM(self.inputs['input'],
+                                                                                   self.parseBoolean(vals['debug']));
+
+        # Propagate Orientation in this weird matrix to image thing
+        self.outputs['output'].affine=self.inputs['input'].affine;
+
+        return True
+
+
+
+