Multi TE support and FBI stability patches (#257)

* Add `echotime` function

* Add TE awareness to DWIParser

* Add `dwiextract` function

Extracts DWI volumes from star:end index

* Add filename dictionary

* Adjust tensor type thresholds

* Add maxFBIBval() method

* Fine tune tensor type thresolhds

* Add fit regime function

Eases full automation of pipeline

* Fix #232 by mitigating large values

* Incorporate fit regime into main

* Fix #255 by introducing overflow mitigation

* Introduce proper indexing of b-value shells in FBI/FBWM

* Add more proper handling of b-value shells

* Add multi-TE support to main

* Minor documentation changes

* Disable B0 exclusion in IRLLS

* Update version to RC10

* Update filenaming algorithm

* Add doc files

* Update CHANGELOG

* Remove unused print statement

* Add `--no_rectify` flag

* Update CHANGELOG

* Update documentation

CHANGELOG.rst

@@ -4,6 +4,43 @@ Changelog
 All notable changes to this project will be documented in this file or
 page
 
+`v1.0-RC10`_
+-----------
+
+Jun 29, 2021
+
+**Added**:
+
+* Support for multi echo time (TE) datasets. PyDesigner will now
+  preprocess DWIs with multiple TEs together, but extract diffusion
+  metrics for each TE separately. Users need to parse :code:`-te`
+  flag to enable this feature.
+* Added :code:`dwiextract` function to *mrpreproc.py* to allowing
+  splitting of *.mif* files.
+* Added function :code:`fit_regime` to *dwipy.py* to automatically run
+  all tensor fitting steps in an appropriate manner.
+* Added :code:`highprecisionpower` to *dwipy.py* to mitigate integer
+  overflow error when performing FBI fODF calculation.
+* Flag :code:`--no_rectify` to disable rectification of FBI fODFs. In
+  some cases where FBI acquistion is excellent, rectification can
+  degrade fODFs instead. This flag is intended to disable
+  rectification of such datasets.
+
+
+**Changed**
+
+* Maximum DKI b-value threshold has been raised to 3,000 mm/s^2,
+  thereby enabling DKI support for researchers using b-values higher
+  than 2,000 mm/s^2 but less than 3,000 mm/s^2.
+* IRLLS now also includes B0 volumes when evaluating goodness-of-fit
+  to make outlier detection more robust and accurate.
+* Various stability patches for FBI and FBWM to ensure error-free
+  extraction of FBI/FBWM metrics.
+
+**Removed**
+
+* None
+
 `v1.0-RC9`_
 -----------
 
@@ -29,7 +66,7 @@ Feb 15, 2021
 
 **Added**:
 
-* Added missing Rician preprocessing to `-s, --standard`
+* Added missing Rician preprocessing to :code:`-s, --standard`
   preprocessing
 
 **Changed**
@@ -331,6 +368,7 @@ Initial port of MATLAB code to Python. 200,000,000,000 BCE
 
 .. Links
 
+.. _v1.0-RC10: https://github.com/m-ama/PyDesigner/releases/tag/v1.0-RC10
 .. _v1.0-RC9: https://github.com/m-ama/PyDesigner/releases/tag/v1.0-RC9
 .. _v1.0-RC8: https://github.com/m-ama/PyDesigner/releases/tag/v1.0-RC8
 .. _v1.0-RC7: https://github.com/m-ama/PyDesigner/releases/tag/v1.0-RC7

designer/fitting/dwi_fnames.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+_dti_ = {
+    'md': 'dti_md',
+    'rd': 'dti_rd',
+    'ad': 'dti_ad',
+    'fa': 'dti_fa',
+    'fe': 'dti_fe',
+    'trace': 'dti_trace'
+}
+
+_dki_ = {
+    'mk': 'dki_mk',
+    'rk': 'dki_rk',
+    'ak': 'dki_ak',
+    'kfa': 'dki_kfa',
+    'mkt': 'dki_mkt',
+    'trace': 'dki_trace'
+}
+
+_wmti_ = {
+    'awf': 'wmti_awf',
+    'eas_ad': 'wmti_eas_ad',
+    'eas_rd': 'wmti_eas_rd',
+    'eas_tort': 'wmti_eas_tort',
+    'ias_da': 'wmti_ias_da'
+}
+
+_fbi_ = {
+    'zeta': 'fbi_zeta',
+    'faa': 'fbi_faa',
+    'sph': 'fbi_fodf',
+    'tract': 'fbi_tractography_dsi',
+    'awf': 'fbwm_awf',
+    'Da': 'fbwm_da',
+    'De_mean': 'fbwm_de_mean',
+    'De_ax': 'fbwm_de_ax',
+    'De_rad': 'fbwm_de_rad',
+    'fae': 'fbwm_fae',
+    'min_cost': 'fbwm_minCost',
+    'min_cost_fn': 'fbwm_minCost_FN'
+}
+
+_tensor_ = {
+    'DT': 'DT',
+    'KT': 'KT'
+}
+
+_outliers_ = {
+    'IRLLS': 'outliers_irlls',
+    'AKC': 'outliers_akc'
+}