pipeline.md

+# Pipeline
+
+The purpose of this wiki page is to write down whole pipeline steps with required input and outputs and check if steps fits together (that previous steps produce enough data for next step).
+
+## Steps
+
+### Segmentation
+
+***Input***
+
+Zip file. We assume that this file will be uploaded for concrete patient. 
+
+***Output***
+
+Zip file with set of `off` files, `bmp`s and one `lmk`. Example structure looks as follow:
+
+```
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV_AVAMinAreaCut_0.47.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV_AVAMinAreaCut_0.47.off
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV_MaxBulbusContour_5.75.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV_MaxBulbusContour_5.75.lmk
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV_MaxBulbusContour_5.75.off
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.off
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.ortho1.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.ortho2.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.ortho3.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve1a.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve1b.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve1c.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve1d.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve1e.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve1f.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve2a.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve2b.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve2c.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve2d.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve2e.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap_finalAV.valve2f.bmp
+0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008.adap.off
+```
+
+Where `0_24a6022d-36f4-4024-95fd-5d9d60e6cc46_imaging_patient_1008` is an prefix specific for segmentation run.
+
+
+### Blood flow simulation
+
+Code contributed by Martain at the beginning of the project (most probably it does not fit to flagship pipeline)
+
+***Input***
+
+```
+fluidFlow.cas
+structural_vent.dat
+```
+
+***Output***
+
+```
+fluidFlow.*.dat
+fluidFlow.*.cas
+```
+
+### Parameter estimation
+
+Not ready yet - no response from Roel yet - we should ask him about it during next EurValve meeting
+
+### Heart Simulation
+
+***Input***
+
+```
+0DModel_input.csv
+```
+
+***Output***
+
+```
+Outfile.csv
+```
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