surfacetopography 0.91.2__py3.6-linux-x86_64.egg

EGG-INFO/PKG-INFO

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+Metadata-Version: 1.2
+Name: SurfaceTopography
+Version: 0.91.2
+Summary: Read and analyze surface topographies
+Home-page: UNKNOWN
+Author: Lars Pastewka
+Author-email: lars.pastewka@imtek.uni-freiburg.de
+License: MIT
+Description: UNKNOWN
+Platform: UNKNOWN
+Requires-Python: >=3.5.0

EGG-INFO/SOURCES.txt

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+.gitattributes
+.gitignore
+.install_parallel_netcdf.sh
+.print_netcdf_capabilities.sh
+.travis.before_install.bash
+.travis.before_script.bash
+.travis.yml
+AUTHORS
+LICENSE.md
+MANIFEST.in
+README.md
+env.sh
+pytest.ini
+requirements.txt
+run-tests.py
+setup.py
+.github/workflows/main.yml
+.idea/.gitignore
+.idea/vcs.xml
+SurfaceTopography/ChangeLog.md
+SurfaceTopography/Converters.py
+SurfaceTopography/Generation.py
+SurfaceTopography/HeightContainer.py
+SurfaceTopography/Interpolation.py
+SurfaceTopography/NonuniformLineScan.py
+SurfaceTopography/Special.py
+SurfaceTopography/UniformLineScanAndTopography.py
+SurfaceTopography/__init__.py
+SurfaceTopography/common.py
+SurfaceTopography.egg-info/PKG-INFO
+SurfaceTopography.egg-info/SOURCES.txt
+SurfaceTopography.egg-info/dependency_links.txt
+SurfaceTopography.egg-info/not-zip-safe
+SurfaceTopography.egg-info/requires.txt
+SurfaceTopography.egg-info/top_level.txt
+SurfaceTopography/IO/DI.py
+SurfaceTopography/IO/FromFile.py
+SurfaceTopography/IO/H5.py
+SurfaceTopography/IO/IBW.py
+SurfaceTopography/IO/MI.py
+SurfaceTopography/IO/Matlab.py
+SurfaceTopography/IO/NC.py
+SurfaceTopography/IO/NPY.py
+SurfaceTopography/IO/OPDx.py
+SurfaceTopography/IO/Reader.py
+SurfaceTopography/IO/__init__.py
+SurfaceTopography/Nonuniform/Autocorrelation.py
+SurfaceTopography/Nonuniform/Detrending.py
+SurfaceTopography/Nonuniform/PowerSpectrum.py
+SurfaceTopography/Nonuniform/ScalarParameters.py
+SurfaceTopography/Nonuniform/VariableBandwidth.py
+SurfaceTopography/Nonuniform/__init__.py
+SurfaceTopography/Nonuniform/common.py
+SurfaceTopography/Tools/__init__.py
+SurfaceTopography/Tools/common.py
+SurfaceTopography/Uniform/Autocorrelation.py
+SurfaceTopography/Uniform/Detrending.py
+SurfaceTopography/Uniform/Filtering.py
+SurfaceTopography/Uniform/Interpolation.py
+SurfaceTopography/Uniform/PowerSpectrum.py
+SurfaceTopography/Uniform/ScalarParameters.py
+SurfaceTopography/Uniform/VariableBandwidth.py
+SurfaceTopography/Uniform/__init__.py
+SurfaceTopography/Uniform/common.py
+c/autocorrelation.cpp
+c/autocorrelation.h
+c/bicubic.cpp
+c/bicubic.h
+c/module.cpp
+c/patchfinder.cpp
+c/patchfinder.h
+c/stack.h
+c/test_stack.cpp
+docs/Makefile
+docs/conf.py
+docs/contributing.rst
+docs/development.rst
+docs/index.rst
+docs/installation.rst
+docs/make.bat
+docs/testing.rst
+docs/usage.rst
+docs/Figures/geometry.svg
+docs/Figures/geometry_pdf_tex.svg
+examples/bicubic_interpolation.py
+examples/files_xy_width_heights.ipynb
+examples/howto_plot_2D_data.ipynb
+helpers/HurstEstimationNumerics.py
+helpers/HurstEstimationSymbolics.py
+helpers/PowerSpectrumSymbolics.py
+helpers/SurfaceExample.asc
+helpers/SurfaceExampleUnfiltered.asc
+helpers/WindowTest.py
+maintenance/copyright.py
+maintenance/replace_header.py
+maintenance/update_license_headers.sh

EGG-INFO/dependency_links.txt

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+

EGG-INFO/native_libs.txt

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+_SurfaceTopography.cpython-36m-x86_64-linux-gnu.so

EGG-INFO/not-zip-safe

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+

EGG-INFO/requires.txt

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+numpy>=1.11.0
+NuMPI>=0.1.1
+muFFT>=0.10.0
+netCDF4>=1.5.0
+igor
+h5py

EGG-INFO/top_level.txt

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+SurfaceTopography
+_SurfaceTopography
+test

SurfaceTopography/ChangeLog.md

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+
+Change log for SurfaceTopography
+=============================
+
+v0.91.2 (31Jul20)
+-----------------
+
+- BUG: Memory leak in Python bindings for bicubic interpolation
+
+v0.91.1 (23Jul20)
+-----------------
+
+- MAINT: Bumped muFFT dependency to v0.10.0
+
+v0.91.0 (2Jul20)
+----------------
+
+- ENH: return topography with undefined (masked) data filled (#19)
+- ENH: make_sphere has option to put undefined data in standoff or not
+- BUG: Fixed missing dependencies when installed as package (#15)
+- BUG: Fixed error when loading text file with trailing newline (#16)
+- BUG: Fixed wrong error message when loading unknown text file format (#14)
+- BUG: renamed CompoundTopography.array to CompoundTopography.heights (#18)
+
+v0.90.0 (17Jun20)
+-----------------
+
+- Refactored PyCo code into three separate Python modules:
+  SurfaceTopography, ContactMechanics and Adhesion
+- muFFT dependency updated to muFFT-0.9.1
+- Moved documentation from README.md to the docs folder 
+
+v0.57.0 (15May20)
+-----------------
+
+- MAINT: Support for new, rewritten muFFT bindings
+- ENH: Bicubic interpolation of two-dimensional topography maps
+- ENH: Fourier derivative of topography
+- BUG: Computation of plastic area is now parallelized (#303)
+- BUG: Info dictionary mutable from user 
+
+v0.56.0 (26Feb20)
+-----------------
+
+- ENH: Change orientation of some readers such that all topographies
+       look like the image in Gwyddion when plotted with
+       "pcolormesh(t.heights().T)" (#295)
+- BUG: Fixes unknown unit "um" when reading mi file (#296)
+- BUG: Fixes missing channel name for mi files (#294)
+- ENH: generate self-affine random surfaces by specifying the self-affine prefactor (#261, #278, #279)
+- BUG: now fourier synthesis can generate Linescans again (#277, #279)
+
+
+v0.55.0 (14Feb20)
+-----------------
+
+- API: Readers now report channel info in ChannelInfo class,
+       fixes inconsistencies in reporting channel information (#190, #192, #236)
+- ENH: Readers report format identifier and are self-documented (#229, #238)
+- ENH: Readers now support Gwyddion's text export format for English and German locale (#230)
+- ENH: DI reader now read acquisition date and stores it in the info dictionary
+- BUG: DI reader autodetection did not work (#258)
+- BUG: Fixes orientation for DI files (#291)
+- DOC: Added notebook showing how 2D topographies can be plotted
+- TST: Added demo notebook which shows how to plot 2D topographies
+- ENH: adhesive ideal plastic simulations with Softwall system (#260, #283)
+
+v0.54.4 (20Dec19)
+-----------------
+
+- BUG: Fixes missing 'nb_grid_pts' key in channels from IBW reader
+
+v0.54.3 (20Dec19)
+-----------------
+
+- BUG: Fixes assertion because of wrong number of channel names (#252)
+
+v0.54.2 (13Dec19)
+-----------------
+
+- BUG: fix rms_laplacian for periodic topographies (#247)
+
+v0.54.1 (13Dec19)
+-----------------
+
+- ENH: higher order derivative for periodic surface (#234,#227)
+- ENH: new reader for Igor Binary Wave files (IBW) (#224)
+- BUG: opdx reader can now handle binary filestreams (#209)
+- BUG: store and restore periodic flag in NonuniformTopography (#240)
+
+v0.54.0 (06Dec19)
+-----------------
+
+- MAINT: correct installation problems because Eigen repository has moved
+- ENH: anisotropic cubic Green's Functions 
+- BUG: NPY reader can now handle filestreams (#209, NUMPI/#24)
+- BUG: opdx reader can now handle filestreams (#209)
+
+v0.53.1 (21Nov19)
+-----------------
+- API: Detrended Topographies with mode "center" keep is_periodic property. Other modes lead to is_periodic=False. 
+  See pastewka/TopoBank/#347
+
+v0.53.0 (20Nov19)
+-----------------
+
+- API: ability to set periodic property of HeightContainer in reader.topography (#198)
+- API: default window for computing PSD is choosen according to topography.is_periodic (#217)
+- Feature: interpolate_fourier pipeline function
+- API: Default of check_boundaries in FreeSystem is False
+- Bug fix: fourier synthesis had a padding line in the generation of topographies with odd number of points (#202)
+- Bug fix: `topography.rms_curvature` no returns rms_curvature, previously rms_laplacian (#200)
+- gnuplot scripts to plot logger output
+
+v0.52.0 (25Aug19)
+-----------------
+
+- API: Return contact map (the 'active set') from constrained conjugate gradient
+- Bug fix: `assign_patch_numbers` was broken on some configurations since v0.51.2
+
+v0.51.2 (8Aug19)
+----------------
+
+- Bug fix: `assign_patch_numbers` crashed for maps larger that 64k x 64k (#191)
+
+v0.51.1 (7Aug19)
+----------------
+
+- Bug fix: Setting physical_sizes argument in readers (#188)
+- Bug fix: physical_sizes should be None for surfacs without a physical size (#189)
+- Bug fix: Running and testing without mpi4py is now possible (#179)
+- Bug fix: Multiple calls to `topography` method of readers (#187)
+- Method to inspect pipeline (#175)
+- CI: All tests (serial and MPI parallel) pass in Travis CI
+
+v0.51.0 (5Aug19)
+----------------
+
+- Cleanup of new reader API
+
+v0.50.2 (1Aug19)
+----------------
+
+- Bug fix: Missing `channel` argument for `topography` method of `WrappedReader` (#181)
+- `WrappedReader` now uses 'Default' as channel name
+
+v0.50.1 (1Aug19)
+----------------
+
+- Bug fix: Running without an MPI installation
+- Bug fix: Reading DI files with non-topographic data (#338)
+
+v0.50.0 (31Jul19)
+-----------------
+
+Overview:
+
+- MPI parallelization of topographies, substrates and interaction.
+- Updated reader framework that supports loading files in parallel. This requires to peek at the files (without
+  loading them) to understand the number of grid points to decide on a domain decomposition strategy.
+
+Technical:
+
+- Use MPI wrapper provided by NuMPI (https://github.com/IMTEK-Simulation/NuMPI) for serial calculations.
+- Switch to parallel L-BFGS of NuMPI. 
+- Removed Cython dependencies. (Parallel) FFT is now handled by muFFT (https://gitlab.com/muspectre/muspectre).
+- Tests have been partially converted to pytest. Parallel tests are run through run-tests
+  (https://github.com/AntoineSIMTEK/runtests).
+
+v0.32.0 (15Jul19)
+-----------------
+
+- Autocorrelation and power-spectrum updates. Both now have an option 'algorithm' that let's the user select
+  between a (fast) FFT and a (slow) brute-force implementation.
+  
+v0.31.3 (7Jul19)
+----------------
+
+- Removed check for existing forces on boundaries (nonperiodic calculations only).
+
+v0.31.1 (20May19)
+-----------------
+
+- Bug fix: Contact calculations now also run with detrended/scaled topographies.
+- Updated hard wall command line script to new topography interface.
+
+v0.31.0 (5Mar19)
+----------------
+
+- Added height-difference autocorrelation and variable bandwidth analysis for nonuniform
+  line scans.
+- Added wrapper 'to_nonuniform' function that turns uniform into nonuniform line scans.
+- Bug fix: 'center' detrend mode for nonunform line scans now minimizes rms height.
+
+v0.30.0 (15Feb19)
+-----------------
+
+Overview:
+
+- Added non-uniform line scans, which can be loaded from text files or constructed from arrays.
+- New class structure for topographies and line scans (for easier maintenance).
+- Major API changes and several bug fixes (see below).
+- Added Hardwall simulation tutorial.
+- Added calculation for second derivative and RMS curvature for nonuniform topographies.
+- Added coordination counting for contact patches. 
+- Simplified computation of perimeter using coordination counting.
+- Started Sphinx documentation with notes how to use the package.
+
+API Changes:
+
+- New API for generating topographies and line scans (height containers) from data, 
+  please use "from PyCo Topography import Topography, NonlinearLineScan, UniformLineScan" now.
+- New API for building pipelines using methods on height containers, e.g. "topography.scale(2).detrend()".
+- Uniform topographies and line scans can be periodic.
+- Removed unit property from height containers. Units are now stored in the info dictionary,
+  which has to be set on generation of the height container.
+- All topographies must have a physical_sizes. Readers use the resolution as the default physical_sizes 
+  if the files contain no physical_sizes information. 
+- Removed 'shape' alias to 'resolution' property for height containers.
+- Size + shape are now always tuples, physical_sizes is also always set as tuple.
+- Topographies can now be pickled and unpickled.  
+- Replaced class 'Sphere' with generator function 'make_sphere'.
+- Contact with "FreeFFTElasticHalfSpace": 
+  Now an error is raised when points at the outer ring of the surface are interacting. 
+  See notebook "examples/Hardwall_Simulation.ipynb".
+  
+Bug fixes:
+   
+- periodicity was ignored in calculation of the distance between contact patches in `distance_map`
+- computation of energy in fourier space didn't match the computation of energy in real space 
+  (however it is not used in actual simulation)   
+- Removed keyword "full_output" from shift_and_tilt().
+- Text files without spaces at beginning of line can be read now.
+- Enable reading topography data from memory buffers and from binary streams.
+- Calculation of 2D autocorrelation function was broken, e.g. radial average.
+- 1D autocorrelation was broken for nonperiodic calculations.
+
+
+v0.18.0 (31Oct18)
+-----------------
+
+- Refactored "Surface" to "Topography".
+- Bug fix: Corrected computation of attractive contact area in Smooth contact system.
+- Bug fix: Corrected computation of inflexion point in LJ93 and VW82 smoothed potentials.
+
+v0.17.0 (06Jul18)
+-----------------
+
+- Height-difference autocorrelation function.
+
+v0.16.0 (23Oct17)
+-----------------
+
+- PyCo now licensed under MIT license.
+
+v0.15.0 (06Sep17)
+-----------------
+
+- Implemented substrates of finite thickness.
+- Support for additional DI file formats.
+- More clever unit conversion in DI files.
+
+v0.14.1 (16Jun17)
+-----------------
+
+- macOS compatibility fixes.
+- Automatic conversion from hardness value (given in units of pressure)
+  into internal units in constrained CG solver.
+
+v0.14.0 (14Mar17)
+-----------------
+
+- Added penetration hardness model for simple plastic calculations.
+
+v0.13.1 (07Mar17)
+-----------------
+
+- Bug fix: Periodic Green's function offset by one lattice constant.
+
+v0.13.0 (13Jan17)
+-----------------
+
+- Added further adhesive reference models (Maugis-Dugdale type models for
+  cylinder and wedge).
+- Added callback option for Polonsky & Keer optimizer.
+- setup.py now has '--openmp' option that triggers compilation of shared-memory
+  (OpenMP) parallel code.
+
+v0.12.0 (05Dec16)
+-----------------
+
+- Main enhancement: Support for masked_arrays in NumpySurface. This allows to
+  have undefined (missing) data points in surfaces. Polonsky & Keer can handle
+  this now.
+- Polonsky & Keer can now optimize at constant pressure (in addition to
+  constant displacement)
+- Updated hard wall script to accept command line arguments.
+- Moved scripts to new 'commandline' folder.
+- Added plotmap.py, tool for plotting surfaces from the command line.
+- Added plotpsd.py, tool for plotting the PSD of a surface from the command
+  line.
+
+v0.11.0 (21Sep16)
+-----------------
+
+- Renamed TiltedSurface to DetrendedSurface.
+
+v0.10.3 (16Sep16)
+-----------------
+
+- Added reader for HGT files (topography data from NASA Shuttle Radar Topography
+  Mission).
+- Bug fix in deprecated 'set_size' that broke hard wall example.
+
+v0.10.2 (29Aug16)
+-----------------
+
+- Added reader for MATLAB files.
+
+v0.10.1 (22Aug16)
+-----------------
+
+- Added 'center' detrending mode which just subtracts the mean value.
+- Added getter and setter for detrend_mode.
+- Added function to return string representation of subtracted plane.
+- Added area_per_pt property to Surface object.
+
+v0.10.0 (31Jul16)
+-----------------
+
+- Exponential adhesion potential from Martin's contact mechanics challenge, to
+  be used in combination with hard-wall (bounded L-BFGS). Added tests for this
+  potential. Thanks go to Joe Monty for implementing this.
+- Surfaces now have a *unit* property, that can be any object but will likely
+  be a string in many cases.
+- Readers now create NumpySurface with *raw* data and wrap it into a
+  ScaledSurface to convert to proper unit.
+- Travis-CI integration
+
+v0.9.4 (27Apr16)
+----------------
+
+- Greenwood-Tripp reference solution
+- Many bug fixes in topography file readers
+
+v0.9.3 (20Mar16)
+----------------
+
+- Wyko OPD reader (.opd)
+- Digital Instruments Nanoscope reader (.di)
+- Igor Binary Wave reader (.ibw)
+- Detrending
+
+v0.9.2 (06Mar16)
+----------------
+
+- X3P reader (.x3p)
+- Automatic file format detection

SurfaceTopography/Converters.py

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+#
+# Copyright 2019-2020 Lars Pastewka
+#           2019 Antoine Sanner
+#
+# ### MIT license
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+
+"""
+Utility function for conversion between uniform and nonuniform
+representations.
+"""
+
+import numpy as np
+
+from .HeightContainer import DecoratedTopography, UniformTopographyInterface, \
+    NonuniformLineScanInterface
+from .NonuniformLineScan import NonuniformLineScan
+from .UniformLineScanAndTopography import UniformLineScan
+
+
+class WrapAsNonuniformLineScan(DecoratedTopography,
+                               NonuniformLineScanInterface):
+    """
+    Wrap a uniform topography into a nonuniform one.
+    """
+
+    def __init__(self, topography, info={}):
+        """
+        Parameters
+        ----------
+        topography : :obj:`NonuniformLineScan`
+            SurfaceTopography to wrap.
+        """
+        super().__init__(topography, info=info)
+
+        # This is populated with functions from the nonuniform topography, but
+        # this is a uniform topography
+        self._functions = NonuniformLineScan._functions
+
+    # Implement abstract methods of AbstractHeightContainer
+
+    @property
+    def dim(self):
+        return 1
+
+    @property
+    def physical_sizes(self):
+        s, = self.parent_topography.physical_sizes
+        p, = self.parent_topography.pixel_size
+        return s - p,
+
+    @property
+    def is_periodic(self):
+        return False
+
+    # Implement nonuniform line scan interface
+
+    @property
+    def nb_grid_pts(self):
+        return self.parent_topography.nb_grid_pts
+
+    @property
+    def x_range(self):
+        s, = self.parent_topography.physical_sizes
+        p, = self.parent_topography.pixel_size
+        return 0, s - p
+
+    def positions(self):
+        """
+        Returns array containing the lateral positions.
+        """
+        r, = self.parent_topography.nb_grid_pts
+        p, = self.parent_topography.pixel_size
+        return np.arange(r) * p
+
+    def heights(self):
+        """
+        Returns array containing the topography data.
+        """
+        return self.parent_topography.heights()
+
+
+class UniformlyInterpolatedLineScan(DecoratedTopography,
+                                    UniformTopographyInterface):
+    """
+    Interpolate a topography onto a uniform grid.
+    """
+
+    def __init__(self, topography, nb_points, padding, info={}):
+        """
+        Parameters
+        ----------
+        topography : :obj:`SurfaceTopography` or :obj:`UniformLineScan`
+            SurfaceTopography to interpolate.
+        nb_points : int
+            Number of equidistant grid points.
+        padding : int
+            Number of padding grid points, zeros appended to the data.
+        """
+        super().__init__(topography, info=info)
+        self.nb_points = nb_points
+        self.padding = padding
+
+        # This is populated with functions from the nonuniform topography, but
+        # this is a uniform topography
+        self._functions = UniformLineScan._functions
+
+    def __getstate__(self):
+        """ is called and the returned object is pickled as the contents for
+            the instance
+        """
+        state = super().__getstate__(), self.nb_points, self.padding
+        return state
+
+    def __setstate__(self, state):
+        """ Upon unpickling, it is called with the unpickled state
+        Keyword Arguments:
+        state -- result of __getstate__
+        """
+        superstate, self.nb_points, self.padding = state
+        super().__setstate__(superstate)
+
+    # Implement abstract methods of AbstractHeightContainer
+
+    @property
+    def dim(self):
+        return 1
+
+    @property
+    def physical_sizes(self):
+        s, = self.parent_topography.physical_sizes
+        return s * (self.nb_points + self.padding) / self.nb_points,
+
+    @property
+    def is_periodic(self):
+        return False
+
+    @property
+    def is_uniform(self):
+        return True
+
+    # Implement uniform line scan interface
+
+    @property
+    def nb_grid_pts(self):
+        """Return nb_grid_pts, i.e. number of pixels, of the topography."""
+        return self.nb_points + self.padding,
+
+    @property
+    def pixel_size(self):
+        return (s / r for s, r in zip(self.physical_sizes, self.nb_grid_pts))
+
+    @property
+    def area_per_pt(self):
+        return self.pixel_size
+
+    @property
+    def has_undefined_data(self):
+        return False
+
+    def positions(self):
+        left, right = self.parent_topography.x_range
+        size = right - left
+        return np.linspace(left - size * self.padding / (2 * self.nb_points),
+                           right + size * self.padding / (2 * self.nb_points),
+                           self.nb_points + self.padding)
+
+    def heights(self):
+        """ Computes the rescaled profile.
+        """
+        x = self.positions()
+        return np.interp(x, *self.parent_topography.positions_and_heights())
+
+
+# Register pipeline functions from this module
+UniformTopographyInterface.register_function('to_nonuniform',
+                                             WrapAsNonuniformLineScan)
+NonuniformLineScanInterface.register_function('to_uniform',
+                                              UniformlyInterpolatedLineScan)