123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122 |
- # Ajayrama Kumaraswamy, 2017, LMU Munich
- """
- The input parameters of different Algorithms
- """
- # **********************************************************************************************************************
- """
- Parameters of Reg-MaxS.
- refSWC: string. The reference SWC file, to which testFile is registered.
- Must be a valid SWC file on the file system.
- testSWC: string. The test SWC file which is registered to refSWC.
- Must be a valid SWC file on the file system.
- resFile: string. This file will be created and the resulting SWC will be written into it.
- It needs to be valid file reference.
- gridSizes: list of floats. These are the voxel sizes over which Reg-MaxS is run.
- Values must be in micrometers.
- transBounds: three member list, each element is a two member list. These members must be floats.
- They are bounds used for estimating translation parameters along XYZ axes.
- Values must be in micrometers.
- transMinRes: float. After searching at the three voxel sizes in gridSizes, a further search is carried
- out at this resolution for translation parameters. Values must be in micrometers.
- rotBounds: three member list, each element is a two member list. These members must be floats.
- They are bounds used for estimating rotation parameters about XYZ axes.
- Values must be in radians.
- rotMinRes: float. After refining rotation parameters at the three voxel sizes in gridSizes, a further
- refinement is carried out at this resolution. Values must be in radians.
- scaleBounds: three member list, each element is a two member list. These members must be floats.
- They are bounds used for estimating scaling parameters along XYZ axes.
- minScaleStepSize: float. After refining scaling parameters at the three voxel sizes in gridSizes, a further
- refinement is carried out at this resolution.
- nCPU: int. Reg-MaxS internally uses multiple processes for exhaustive searches.
- This specifies the number of processes to use. It can be a maximum of number of
- processors on the machine being used. Larger this number, faster the execution.
- inPartsDir: string. A file system directory, the swc files in which are transformed exactly the same as
- testSWC and written into outPartsDir.
- outPartsDir: string. A file system directory into which the transformed swc files of inPartsDir are written.
- It will be created if it does not exist.
- retainTempFiles: boolean. Reg-MaxS generates some temporary files in the directory where resFile is supposed to
- be created. If retainTempFiles is True, these are not deleted. Else, they are.
- """
- RegMaxSParNames = ['refSWC', 'testSWC', 'resFile',
- 'gridSizes',
- 'transBounds', 'transMinRes',
- 'rotBounds', 'rotMinRes',
- 'scaleBounds', 'minScaleStepSize',
- 'nCPU', 'inPartsDir', 'outPartsDir', 'retainTempFiles']
- # **********************************************************************************************************************
- """
- Parameters of Reg-MaxS-N. Some parameters are same as of Reg-MaxS above and hence are omitted here.
- swcList: list of strings. Each member must refer to a valid SWC file on the file system.
- initRefSWC: string. The initial reference to use for Reg-MaxS-N, i.e., the reference of the first iteration.
- Must be a valid SWC file on the file system.
- resDir: string. The directory into which the results of Reg-MaxS-N are written. Will be created anew
- or replaced if it exists.
- finallyNormalizeWRT: string. Must be one of the SWCs of swcList. The whole set of SWCs after registration
- is transformed affinely together so that this SWC is restored to it's final form.
- maxIter: int. The number of iterations for which Reg-MaxS-N runs before stopping and returning the
- result.
- usePartsDir: boolean. If True, Reg-MaxS-N check if for every SWC in swcList, a folder exists with the
- same name and path without the '.swc' extention. If such folders exist, the SWCs in them are
- transformed exactly the same as their corresponding SWCs and written into folders with the same
- name in resDir.
- """
- RegMaxSNParNames = [
- 'swcList', 'initRefSWC', 'resDir', 'finallyNormalizeWRT', 'maxIter',
- 'gridSizes',
- 'transBounds', 'transMinRes',
- 'rotBounds', 'rotMinRes',
- 'scaleBounds', 'minScaleStepSize',
- 'nCPU', 'usePartsDir'
- ]
- # **********************************************************************************************************************
- """
- Parameters of the registration PCA-based algorithm. Some parameters have the same meaning as in Reg-MaxS above and
- hence have been omitted here.
- gridSizes: list of floats. These are the voxel sizes over which Reg-MaxS is run.
- Values must be in micrometers. These values are not used in the actual algorithm. The last
- element of this list is used to calculate a measure of dissimilarity between the reference SWC
- and the result SWC produced by the 'pcaBased' algorithm.
- usePartsDir: boolean. If True, Reg-MaxS-N check if for every SWC in swcList, a folder exists with the
- same name and path without the '.swc' extention. If such folders exist, the SWCs in them are
- transformed exactly the same as their corresponding SWCs and written into folders with the same
- name in resDir.
- """
- pcaBasedParNames = [
- 'refSWC', 'testSWC', 'resFile',
- 'gridSizes', 'usePartsDir'
- ]
- # **********************************************************************************************************************
- DensitySaveParNames = ['refSWC', 'resFile']
|