various small fixes (#442)

stestoll · web-flow · commit 704b8dcb9dba · 2023-08-09T19:40:00.000+02:00
diff --git a/deerlab/bg_models.py b/deerlab/bg_models.py
@@ -129,7 +129,7 @@ def _hom3d(t,conc,lam):
 The expression for this model is
 
 .. math::
-   B(t) = \mathrm{exp}\left(i \frac{8\pi}{9\sqrt{3}}(\sqrt{3} + \mathrm{ln}(2-\sqrt{3}))\lambda c_s D t\right)
+   B(t) = \mathrm{exp}\left(\mathrm{i}\frac{8\pi}{9\sqrt{3}}(\sqrt{3} + \mathrm{ln}(2-\sqrt{3}))\lambda c_s D t\right)
 
 where `c_s` is the spin concentration (entered in spins/m\ :sup:`3` into this expression) and D is the dipolar constant
 
diff --git a/deerlab/utils.py b/deerlab/utils.py
@@ -78,7 +78,7 @@ def parse_multidatasets(y_, A, weights, noiselvl, precondition=False, masks=None
     prescales = np.ones(nDatasets)
     for i in range(nDatasets):
         if precondition:
-            prescales[i] = max(V[i])
+            prescales[i] = max(y[i])
             ylist.append(y[i]/prescales[i])
         else:
             ylist.append(y[i])
diff --git a/docsrc/README.md b/docsrc/README.md
@@ -23,15 +23,15 @@ In order to compile the documentation the following steps must be followed:
         pip install sphinx-design
 
 5) Download and install [dvisvgm](https://dvisvgm.de/Downloads/).
-		
+
 ### Runnning the Sphinx builder
 
 To build the documentation from the source, call the `Makefile` or `make.bat` scripts:
 
         # To compile using the cached data
         ./docsrc/make.bat
         # To compile from scratch
-        ./docsrc/make.bat clean    
+        ./docsrc/make.bat clean 
 
 If the `sphinx-build` command is not found, the documentation can be built with the following command 
 
diff --git a/docsrc/source/basics.rst b/docsrc/source/basics.rst
@@ -8,7 +8,7 @@ All functions in DeerLab use the same units: all distances are in units of **nan
 Distance distributions
 *********************************
 
-A distance distribution `P(r)` between two spins is represented by a pair of vectors: a distance vector ``r`` (in nanometers) and a vector of densities ``P`` (in inverse nanometers). The distance vector ``r`` can have linearly or non-linearly increasing values, but must have positive non-zero values. The elements ``P[i]`` are the distance distribution values at ``r[i]`` and are posiive or zero. Outside of the range defined by ``r``, the distribution ``P`` is assumed to be zero, i.e. the distribution is truncated to the range ``r``. The distance distribution ``P`` is normalized such that the integral over the range of the provided ``r`` equals one:
+A distance distribution `P(r)` between two spins is represented by a pair of vectors: a distance vector ``r`` (in nanometers) and a vector of densities ``P`` (in inverse nanometers). The distance vector ``r`` can have linearly or non-linearly increasing values, but must have positive non-zero values. The elements ``P[i]`` are the distance distribution values at ``r[i]`` and are positive or zero. Outside of the range defined by ``r``, the distribution ``P`` is assumed to be zero, i.e. the distribution is truncated to the range ``r``. The distance distribution ``P`` is normalized such that the integral over the range of the provided ``r`` equals one:
 
 .. math:: \int_{r_\mathrm{min}}^{r_\mathrm{max}} P(r) \mathrm{d}r = 1
 
diff --git a/docsrc/source/changelog.rst b/docsrc/source/changelog.rst
@@ -108,32 +108,32 @@ Release ``v1.0.0`` - December 2022
 
 .. rubric:: ``fit``
 
-  - |enhancement| The function now returns a full uncertainty quantification for the normalization factor of any model parameter with a normalization condition (:pr:`372`).
-  - |efficiency| |api| Removes the automatic computation of the ``modelUncert`` output containing the propagated uncertainty estimate of the model's response (:pr:`401`). This significantly speeds up the runtime of the function by disabling the automatic propagation of uncertainty to the model's response which could take from several seconds to several minutes in complex models (:issue:`391`).
+- |enhancement| The function now returns a full uncertainty quantification for the normalization factor of any model parameter with a normalization condition (:pr:`372`).
+- |efficiency| |api| Removes the automatic computation of the ``modelUncert`` output containing the propagated uncertainty estimate of the model's response (:pr:`401`). This significantly speeds up the runtime of the function by disabling the automatic propagation of uncertainty to the model's response which could take from several seconds to several minutes in complex models (:issue:`391`).
 
 
 .. rubric:: ``dipolarkernel``
 
-  - |feature| Implements multi-spin dipolar pathways up to three-spin interactions (:pr:`385`). The function takes now a list of distance vectors ``[r1,r2,...,rQ]`` for multi-spin kernels. 
-  - |feature| Expands the function to be able to account for arbitrary experimental time coordinates (:pr:`385`). Now a list of time vectors ``[t1,t2,...,tD]`` can be specified to construct a D-dimensional dipolar kernel.
-  - |enhancement| : Refactors most code in the function (:pr:`385`). THe code should now be more logically ordered using mathematical symbols for clearer equations. 
-  - |api| Introduces a new and clearer syntax for defining dipolar pathways (:pr:`385`). Now, instead of specifying a list of pathways, where each pathway is a list of values (being the amplitude, refocusing time, and harmonic in that order), now pathways are specified as a list of dictionaries, e.g. ``pathways = [{'amp':0.5}, 'reftime':0, 'harmonic':1]``.
-  - |feature| |efficiency| Adds a new optional argument ``tinterp`` to construct a dipolar kernel for a pathway and interpolate other pathways from that one (:pr:`393`). 
+- |feature| Implements multi-spin dipolar pathways up to three-spin interactions (:pr:`385`). The function takes now a list of distance vectors ``[r1,r2,...,rQ]`` for multi-spin kernels. 
+- |feature| Expands the function to be able to account for arbitrary experimental time coordinates (:pr:`385`). Now a list of time vectors ``[t1,t2,...,tD]`` can be specified to construct a D-dimensional dipolar kernel.
+- |enhancement| : Refactors most code in the function (:pr:`385`). THe code should now be more logically ordered using mathematical symbols for clearer equations. 
+- |api| Introduces a new and clearer syntax for defining dipolar pathways (:pr:`385`). Now, instead of specifying a list of pathways, where each pathway is a list of values (being the amplitude, refocusing time, and harmonic in that order), now pathways are specified as a list of dictionaries, e.g. ``pathways = [{'amp':0.5}, 'reftime':0, 'harmonic':1]``.
+- |feature| |efficiency| Adds a new optional argument ``tinterp`` to construct a dipolar kernel for a pathway and interpolate other pathways from that one (:pr:`393`). 
 
 .. rubric:: ``dipolarbackground``
 
-  - |feature| Implements multi-spin dipolar pathways up to three-spin interactions (:pr:`385`).
-  - |feature| Expands the function to be able to account for arbitrary experimental time coordinates (:pr:`385`). Now a list of time vectors ``[t1,t2,...,tD]`` can be specified to construct a D-dimensional dipolar background function.
-  - |api| Introduces the same new syntax for defining dipolar pathways as in ``dipolarkernel`` (:pr:`385`).
+- |feature| Implements multi-spin dipolar pathways up to three-spin interactions (:pr:`385`).
+- |feature| Expands the function to be able to account for arbitrary experimental time coordinates (:pr:`385`). Now a list of time vectors ``[t1,t2,...,tD]`` can be specified to construct a D-dimensional dipolar background function.
+- |api| Introduces the same new syntax for defining dipolar pathways as in ``dipolarkernel`` (:pr:`385`).
 
 
 .. rubric:: ``correctphase``
 
-  - Adds a new optional argument ``offset`` to enable a numerical optimization of the phase while accounting for a non-zero imaginary component offset (:issue:`392`, :pr:`395`).
+- Adds a new optional argument ``offset`` to enable a numerical optimization of the phase while accounting for a non-zero imaginary component offset (:issue:`392`, :pr:`395`).
 
 .. rubric:: ``snlls``
 
-  - Adds an optional argument ``modeluq`` to enable /disable the model uncertainty propagation (:pr:`401`).
+- Adds an optional argument ``modeluq`` to enable /disable the model uncertainty propagation (:pr:`401`).
 
 Release ``v0.14.5`` - December 2022
 ------------------------------------------
@@ -143,12 +143,12 @@ Release ``v0.14.5`` - December 2022
 
 .. rubric:: ``fit``
 
-  - |fix| Expose the ``cores`` option of ``bootstrap_analysis`` to parallelize bootstrap analysis from the ``fit`` function (:pr:`387`).
-  - |fix| Correct behavior of masking during fitting (:pr:`394`). When using the ``mask`` option of the ``fit`` function, certain steps such as noise estimation and goodness-of-fit assessment were not taking into account the mask during the analysis.
+- |fix| Expose the ``cores`` option of ``bootstrap_analysis`` to parallelize bootstrap analysis from the ``fit`` function (:pr:`387`).
+- |fix| Correct behavior of masking during fitting (:pr:`394`). When using the ``mask`` option of the ``fit`` function, certain steps such as noise estimation and goodness-of-fit assessment were not taking into account the mask during the analysis.
 
 .. rubric:: ``bootstrap_analysis``
 
-  - |fix| Fix error prompted when analyzing scalar variables (:pr:`402`).
+- |fix| Fix error prompted when analyzing scalar variables (:pr:`402`).
 
 
 
@@ -163,11 +163,11 @@ Release ``v0.14.4`` - August 2022
 
 .. rubric:: ``fit``
 
-  - |fix| Added multiple missing optional keyword arguments to the documentation of the function (:pr:`367`).
+- |fix| Added multiple missing optional keyword arguments to the documentation of the function (:pr:`367`).
 
 .. rubric:: ``dd_randcoil``
 
-  - |fix| Fixed the erronously switched descriptions of the model parameters (:pr:`361`).
+- |fix| Fixed the erronously switched descriptions of the model parameters (:pr:`361`).
 
 
 
@@ -296,52 +296,52 @@ Release ``v0.14.0`` - April 2022
 
 .. rubric:: ``bootstrap_analysis``
 
-  - |efficiency| Added a new keyword argument ``memorylimit`` to specify the maximal memory used by the bootstrap analysis (by default 8GB). If the total analysis is expected to exceed the memory limit, the function will abort the execution (:issue:`200`, :pr:`238`).
+- |efficiency| Added a new keyword argument ``memorylimit`` to specify the maximal memory used by the bootstrap analysis (by default 8GB). If the total analysis is expected to exceed the memory limit, the function will abort the execution (:issue:`200`, :pr:`238`).
 
 .. rubric:: ``dipolarkernel``
 
-  - |feature| Added a new option `complex` to request the complex-valued dipolar kernel to simulate the out-of-phase contributions to the dipolar signals (:pr:`258`).
-  - |efficiency| Added a new keyword argument ``memorylimit`` to specify the maximal memory used by the dipolar kernel (by default 8GB). If the dipolar kernel is expected to exceed the memory limit, the function will abort the execution (:issue:`200`, :pr:`238`).
-  - |fix| Prompts error if wrong method is selected when specifying a limited excitation bandwidth (:issue:`181`, :pr:`183`). 
+- |feature| Added a new option `complex` to request the complex-valued dipolar kernel to simulate the out-of-phase contributions to the dipolar signals (:pr:`258`).
+- |efficiency| Added a new keyword argument ``memorylimit`` to specify the maximal memory used by the dipolar kernel (by default 8GB). If the dipolar kernel is expected to exceed the memory limit, the function will abort the execution (:issue:`200`, :pr:`238`).
+- |fix| Prompts error if wrong method is selected when specifying a limited excitation bandwidth (:issue:`181`, :pr:`183`). 
 
 .. rubric:: ``bg_models``
 
-  - |feature| Implemented the time-dependent phase shifts for all the built-in physical background models, namely ``bg_hon3d_phase``, ``bg_hom3dex_phase``, and ``bg_homfractal_phase`` (:pr:`258`).
-  - |enhancement| Changed the implementation of ``bg_hom3dex`` (:pr:`258`). This avoids the use of tabulated pre-calculated values. Accordingly the utility functions ``calculate_exvolume_redfactor`` and ``load_exvolume_redfactor`` have been removed.
-  - |fix| Improved the implementation and behavior of the ``bg_homfractal`` model (:pr:`258`).
+- |feature| Implemented the time-dependent phase shifts for all the built-in physical background models, namely ``bg_hon3d_phase``, ``bg_hom3dex_phase``, and ``bg_homfractal_phase`` (:pr:`258`).
+- |enhancement| Changed the implementation of ``bg_hom3dex`` (:pr:`258`). This avoids the use of tabulated pre-calculated values. Accordingly the utility functions ``calculate_exvolume_redfactor`` and ``load_exvolume_redfactor`` have been removed.
+- |fix| Improved the implementation and behavior of the ``bg_homfractal`` model (:pr:`258`).
 
 .. rubric:: ``diststats``
 
-  - |fix| Fixed the behavior when dealing with distributions with arbitrary integral values
+- |fix| Fixed the behavior when dealing with distributions with arbitrary integral values
 
 .. rubric:: ``selregparam``
 
-  - |enhancement| Implemented a general LSQ solver as backend to adapt to different regularized optimization problem structures.
-  - |enhancement| Generalized the linear least-squares solver. (:pr:`216`).
-  - |enhancement| In the ``brent`` mode, the search range is no longer selected from the min/max of ``regparamrange`` output, but from a new keyword argument ``searchrange`` set by default to ``[1e-8,1e2]``. The default values were chosen as the statistical means of Monte-Carlo simulations of the min/max values of ``regparamrange``'s output for typical 4-pulse DEER kernels (:pr:`232`).
-  - |enhancement|  In the ``grid`` mode, the grid-values are passed by the pre-existing keyword argument ``candidates``. By default, if not specified, a grid will be generated from the ``searchrange`` argument (:pr:`232`).
+- |enhancement| Implemented a general LSQ solver as backend to adapt to different regularized optimization problem structures.
+- |enhancement| Generalized the linear least-squares solver. (:pr:`216`).
+- |enhancement| In the ``brent`` mode, the search range is no longer selected from the min/max of ``regparamrange`` output, but from a new keyword argument ``searchrange`` set by default to ``[1e-8,1e2]``. The default values were chosen as the statistical means of Monte-Carlo simulations of the min/max values of ``regparamrange``'s output for typical 4-pulse DEER kernels (:pr:`232`).
+- |enhancement|  In the ``grid`` mode, the grid-values are passed by the pre-existing keyword argument ``candidates``. By default, if not specified, a grid will be generated from the ``searchrange`` argument (:pr:`232`).
 
 .. rubric:: ``UQResult``
 
-  - |fix| Ensures non-negativity of estimated parameter uncertainty probability density functions.
-  - |enhancement| Improve the behavior of ``UQresult.propagate()`` for bootstrapped uncertainty results. Now, instead of propagating bootstrapped uncertainty via the estimated covariance matrix, the uncertainty is propagated by bootstrapping from the bootstrapped uncertainty distributions (:pr:`218`). 
-  - |fix| Fix behavior of the bootstrap median (:pr:`254`).
-  - |fix| Suppress multiple ``DeprecationWarning`` warnings during uncertainty calculations (:pr:`255`).
-  - |fix| Fix error prompt when requesting private methods such as ``__deepcopy__`` (:issue:`301`, :pr:`303`).
+- |fix| Ensures non-negativity of estimated parameter uncertainty probability density functions.
+- |enhancement| Improve the behavior of ``UQresult.propagate()`` for bootstrapped uncertainty results. Now, instead of propagating bootstrapped uncertainty via the estimated covariance matrix, the uncertainty is propagated by bootstrapping from the bootstrapped uncertainty distributions (:pr:`218`). 
+- |fix| Fix behavior of the bootstrap median (:pr:`254`).
+- |fix| Suppress multiple ``DeprecationWarning`` warnings during uncertainty calculations (:pr:`255`).
+- |fix| Fix error prompt when requesting private methods such as ``__deepcopy__`` (:issue:`301`, :pr:`303`).
 
 .. rubric:: ``correctphase``
 
-  -  |fix| Implement a fully vectorized analytical solution, resulting in a 30-150x speedup (:pr:`256`, :pr:`279`). 
-  - |api| Eliminate the ``phase='posrealint'`` and ``phase='negrealint'`` options (:pr:`279`).
+- |fix| Implement a fully vectorized analytical solution, resulting in a 30-150x speedup (:pr:`256`, :pr:`279`). 
+- |api| Eliminate the ``phase='posrealint'`` and ``phase='negrealint'`` options (:pr:`279`).
 
 .. rubric:: ``deerload``
 
-  - |fix| Raise warning instead of exception when parsing lines without key-value pairs (:pr:`256`). This avoid errors when trying to load BES3T files with PulseSPEL scripts edited in different OS systems.
+- |fix| Raise warning instead of exception when parsing lines without key-value pairs (:pr:`256`). This avoid errors when trying to load BES3T files with PulseSPEL scripts edited in different OS systems.
 
 .. rubric:: ``whitegaussnoise``
 
-  - |api| Renamed the argument ``level`` to ``std`` for clarity (:pr:`276`).
-  - |api| Make the argument ``std`` a required positional argument and no longer provide a default value (:pr:`276`).
+- |api| Renamed the argument ``level`` to ``std`` for clarity (:pr:`276`).
+- |api| Make the argument ``std`` a required positional argument and no longer provide a default value (:pr:`276`).
 
 Release ``v0.13.2`` - July 2021
 ------------------------------------------
