NSFopen 2.4.0__tar.gz → 2.4.1__tar.gz

{nsfopen-2.4.0 → nsfopen-2.4.1}/CHANGELOG.md

@@ -1,141 +1,149 @@
-# Change log
-
-## 2.4.0 (not yet released)
-
-Compared to **2.3.0**.
-
-### Force spectroscopy analysis
-Added, in `NSFopen.process` (the calculations of the Spectroscopy page of NSSA, the NSF Surface and Spectroscopy
-Analyzer, so a script and the program give the same numbers):
-- `contact`: elastic contact of a tip pressed into a flat sample. Models Hertz, Sneddon (exact), DMT, JKR and
-  Oliver-Pharr; tip shapes sphere, cone, four-sided pyramid, flat cylinder punch and hyperboloid. `fit_elastic`,
-  `fit_jkr`, `fit_oliver_pharr` give the Young's modulus, reduced modulus, contact point, adhesion and the fit quality.
-- `spectroscopy`: `SpecFile` opens the force curves and force maps of NID and NHF files. `ForceSettings` and
-  `ForceAnalysis` process them: smoothing, baseline (offset, tilt, or an interference sine with its period found),
-  contact point, indentation, adhesion, pull-off, adhesion and dissipated energy, and the model fit. `Results` has
-  statistics, maps, masks, fits of different models on different regions, a quality filter (leave out fits below an R²)
-  and CSV export. Maps can be analyzed partly (every n-th line and column, or a region).
-- `iv`: I-V curves with dI/dV, normalized conductance, zero-bias conductance and resistance, gap and rectification.
-
-### Color maps
-- 12 maps are defined in `colormaps.py` (`NANOSURF`): Sky (the default for heights), Warm, Flare, Caribbean, Strata,
-  Gold, Digitalis, Neon, Plum, Cold, Spectrum and Maple, plus BlueBlackRed. `register()` adds them and their reversed
-  versions (`Sky_r`) to matplotlib; `colormap(name)` returns any of them or a matplotlib map.
-- The 59 Gwyddion gradient files that 2.3.0 included are removed: they are GPL, NSFopen is MIT. An installed Gwyddion's
-  gradients are found on Windows, macOS and Linux (`gwyddion_dirs`, `gwyddion_gradients`, `register(gwyddion=True)`), and
-  `colors(name)` uses them when the name is not one of the 12.
-
-### Changes that can affect existing scripts
-| What | 2.3.0 | 2.4.0 |
-|---|---|---|
-| `colors(name)` with a Gwyddion name | 59 gradient files in the package | 12 maps defined in the code; `Pm3d`, `Blend2`, `Code-V` open as `Flare`, `Strata`, `Spectrum`; the others only with an installed Gwyddion or `gwy_dir=` |
-| `colormaps.GRADIENTS` | The gradient folder | Removed |
-
-### Examples
-- New `Force_Spectroscopy/Contact_Models.py`: a force map fitted with `process.spectroscopy`, with statistics, the
-  quality filter, maps of the modulus and adhesion, and the stiffest curve with its fit.
-
-### Packaging
-- Credentials (`tokens.json`, `.env`, `*.token`) in the example folders are never packaged.
-
-## 2.3.0 (November 2, 2026)
-
-Compared to **2.2.4**, the latest version on PyPI (August 2024).
-
-### Highlights
-- `pip install NSFopen` now works by itself: the `nanosurf` and `scikit-learn` packages are no longer needed.
-- NID files are read about 5 times faster, and line flattening is about twice as fast.
-- NHF spectroscopy files of any size open immediately, and their curves are read when asked for.
-- WaveMode NMA files are read, with a curve for every pixel and maps of any quantity.
-- `process` has many new image analysis functions, brought over from the Nanosurf Surface Analyzer (now NSSA).
-- Figures take their units and labels from the file, can be placed in subplots, and there is a new 3D plot.
-
-### Reading files
-Added:
-- New NHF reader that needs only h5py, for file versions 1.1 and 2.0 to 2.6. Images are identical to those of Nanosurf's
-  reader on versions 1.1, 2.0, 2.3, 2.4 and 2.6.
-- Spectroscopy (`afm.spec`): segments, grid position, other units through the file's calibration, force curves.
-- WaveMode NMA (`afm.nma`): `curve()` gives Z, interaction and force of a pixel; `map()` builds per-pixel maps.
-- `afm.units` holds the unit of every channel. `afm.close()` releases an NHF file; `read` also works in a `with` block.
-- `read(..., measurement=)` picks a measurement of an NHF file.
-
-Fixed:
-- 2.2.4 needed `nanosurf` to be imported but did not declare it, and failed on NHF files with `nanosurf` 2.0.7.
-- NID headers were read as Latin-1, so units and sizes came out as `°` and `3µm`.
-- Duplicate `Wait` segments of older NHF files overwrote each other: the second is now `Wait 2`.
-- A third NID channel of the same name overwrote the second: they are now `Amplitude`, `Amplitude2`, `Amplitude3`.
-- A truncated NID file now says so.
-
-### Processing images
-Added:
-- Leveling: `level_flatten`, `level_poly2d`, `level_lines`, `level_align_rows`, `level_facet`, `level_three_point`,
-  `level_median`, `level_rolling_ball`, `level_shift`.
-- Filters: `filter_basic`, `filter_median`, `filter_gaussian`, `filter_fft`, `filter_notch`.
-- Glitches: `glitch_spikes`, `glitch_lines`, `glitch_auto_lines`, `glitch_scars`, `glitch_step_lines`, `glitch_fill_mask`.
-- Masks, kept per channel: `set_mask` and `mask_threshold`, `mask_otsu`, `mask_watershed`, `mask_outliers`, `mask_scars`,
-  `mask_shape`, `mask_floodfill`, `mask_grow`, `mask_shrink`, `mask_invert`, `mask_clear`, `mask_remove_small`,
-  `mask_fill_holes`. Leveling, filters and statistics can use the mask.
-- Geometry and scale: `geometry_crop`, `geometry_flip`, `geometry_rotate`, `geometry_resample`, `geometry_square_pixels`,
-  `rescale_scale`, `rescale_z_to_reference`, `rescale_xy`.
-- Statistics after ISO 25178: `statistics`, `bearing_curve`, `histogram_fit`, `slope_distributions`.
-- Lines: `line_profile`, `step_heights`, `critical_dimension`, `masked_step_height`, and `profile_roughness` after
-  ISO 21920.
-- Spectra and texture: `psd`, `psd_fit`, `spectrum`, `acf`, `line_functions`, `rms_by_scale`, `lattice`.
-- Grain analysis: `grains`.
-- Two channels: `combine`, `find_shift`.
-- Access: `channels`, `array`, `set_channel`, `size`, `unit`, `origin`, and `apply` and `operations`.
-
-Fixed:
-- `NSFopen.process` could not be imported, because `colormaps.py` imported itself.
-- `flatten(inplace=False)` and similar calls changed the data as well as returning the result.
-- `plane_level` was wrong on non-square images.
-- The physical sizes of non-square NHF images were swapped.
-
-### Figures
-Added:
-- `plot3d`, a 3D view after the Surface Analyzer's, with materials, lighting and overlays of another channel. It needs no
-  graphics card.
-- `plot_profile`, `plot_psd`, `plot_histogram_fit`, `plot_bearing`, `plot_acf`.
-- `ax=` to draw into subplots, and `figsize`, `dpi`, `theme` and `color_range` on the plots.
-- `image(profile=)` shows where a line cut lies.
-- Color maps by name, including the Gwyddion gradients now included with the package: `cmap='Gold'`.
-
-Fixed:
-- The default scale bar had zero length on scans of about 2.5 µm or less, and non-integer lengths were labelled wrongly.
-- `hist(color=)` raised an error.
-
-### Changes that can affect existing scripts
-| What | 2.2.4 | 2.3.0 |
-|---|---|---|
-| NHF force curves `[row, col]` | Position in the file | True grid position, row 0 at the bottom |
-| NHF force curves | Arrays | Read on access; `np.asarray(curves)` gives the array |
-| `image` and `hist`, `scale` | `1e9` for every channel | A readable unit from the channel; `scale=1e9` still forces it |
-| `hist`, `xlabel` | `Z-Axis [nm]` for every channel | The channel and its unit |
-| `image`, color bar | Only with `cbar=` | Always; `colorbar=False` turns it off |
-| `image`, pixels | matplotlib's default | `interpolation='nearest'`; can be overridden |
-| `remove_outliers` | Nearest neighbors with scikit-learn | Interpolation from the pixels around; the numbers differ, and `neighbors` is gone |
-| Unknown channel | pandas `KeyError` | `ValueError` that lists the channels |
-| Default channel | `Z-Axis` only | Falls back to `Topography` in files that have no `Z-Axis` |
-| `NSFopen.read.checkFileType` | Present | Removed |
-
-`stats()` keeps its results, including `Sku` as excess kurtosis (0 for a Gaussian surface). The new `statistics()` gives
-the ISO value of `Sku` (3 for a Gaussian surface).
-
-### Examples
-- All are rewritten around `process`, and there is a new `Grain_Analysis`.
-- **`Spring_Constant`: the result changes from 14.5 to 24.0 N/m.** The old fit used a power formula on amplitude data and
-  found Q = 253; the file records Nanosurf's own Q of 442, and the corrected fit finds 417.
-- `Plotting_Data`: the image was drawn upside down.
-- `Force_Spectroscopy`: the map axes were labelled µm but showed pixels.
-- `Sharpen_Image`: it no longer passes the data through an 8-bit JPEG, and needs neither OpenCV nor PIL.
-- `Plane_Removal`: it crashed on non-square images, and its clipping changed the data.
-- `Lateral_Force`: the offset between the scans is measured instead of set by hand.
-- Renamed without spaces: `Plotting_Data.py`, `Lateral_Force_Processing.py`, `Sharpen_Image.py`.
-
-### Requirements
-- matplotlib 3.6 or newer; the other requirements are unchanged (numpy, scipy, pandas, h5py, Python 3.9 or newer).
-- Removed: `nanosurf` and `scikit-learn`, which 2.2.4 used without declaring them.
-
-## Earlier versions
-The earlier releases have no change notes. Their list and dates are on
-[PyPI](https://pypi.org/project/NSFopen/#history).
+# Change log
+
+## 2.4.1 (November 4, 2026)
+
+### Fixed
+- Reading a NID file gave a pandas warning (`Series.dropna(inplace=True)` is deprecated from pandas 3.1). The data is
+  the same.
+
+## 2.4.0 (November 4, 2026)
+
+Compared to **2.3.0**.
+
+### Force spectroscopy analysis
+Added, in `NSFopen.process` (the calculations of the Spectroscopy page of NSSA, the NSF Surface and Spectroscopy
+Analyzer, so a script and the program give the same numbers):
+- `contact`: elastic contact of a tip pressed into a flat sample. Models Hertz, Sneddon (exact), DMT, JKR and
+  Oliver-Pharr; tip shapes sphere, cone, four-sided pyramid, flat cylinder punch and hyperboloid. `fit_elastic`,
+  `fit_jkr`, `fit_oliver_pharr` give the Young's modulus, reduced modulus, contact point, adhesion and the fit quality.
+- `spectroscopy`: `SpecFile` opens the force curves and force maps of NID and NHF files. `ForceSettings` and
+  `ForceAnalysis` process them: smoothing, baseline (offset, tilt, or an interference sine with its period found),
+  contact point, indentation, adhesion, pull-off, adhesion and dissipated energy, and the model fit. `Results` has
+  statistics, maps, masks, fits of different models on different regions, a quality filter (leave out fits below an R²)
+  and CSV export. Maps can be analyzed partly (every n-th line and column, or a region).
+- `iv`: I-V curves with dI/dV, normalized conductance, zero-bias conductance and resistance, gap and rectification.
+
+### Color maps
+- 12 maps are defined in `colormaps.py` (`NANOSURF`): Sky (the default for heights), Warm, Flare, Caribbean, Strata,
+  Gold, Digitalis, Neon, Plum, Cold, Spectrum and Maple, plus BlueBlackRed. `register()` adds them and their reversed
+  versions (`Sky_r`) to matplotlib; `colormap(name)` returns any of them or a matplotlib map.
+- The 59 Gwyddion gradient files that 2.3.0 included are removed: they are GPL, NSFopen is MIT. An installed Gwyddion's
+  gradients are found on Windows, macOS and Linux (`gwyddion_dirs`, `gwyddion_gradients`, `register(gwyddion=True)`), and
+  `colors(name)` uses them when the name is not one of the 12.
+
+### Changes that can affect existing scripts
+| What | 2.3.0 | 2.4.0 |
+|---|---|---|
+| `colors(name)` with a Gwyddion name | 59 gradient files in the package | 12 maps defined in the code; `Pm3d`, `Blend2`, `Code-V` open as `Flare`, `Strata`, `Spectrum`; the others only with an installed Gwyddion or `gwy_dir=` |
+| `colormaps.GRADIENTS` | The gradient folder | Removed |
+
+### Examples
+- New `Force_Spectroscopy/Contact_Models.py`: a force map fitted with `process.spectroscopy`, with statistics, the
+  quality filter, maps of the modulus and adhesion, and the stiffest curve with its fit.
+
+### Packaging
+- Credentials (`tokens.json`, `.env`, `*.token`) in the example folders are never packaged.
+
+## 2.3.0 (November 2, 2026, yanked on PyPI)
+
+Yanked because the package included the GPL-licensed Gwyddion gradient files; use 2.4.0 or newer.
+
+Compared to **2.2.4**, the latest version on PyPI (August 2024).
+
+### Highlights
+- `pip install NSFopen` now works by itself: the `nanosurf` and `scikit-learn` packages are no longer needed.
+- NID files are read about 5 times faster, and line flattening is about twice as fast.
+- NHF spectroscopy files of any size open immediately, and their curves are read when asked for.
+- WaveMode NMA files are read, with a curve for every pixel and maps of any quantity.
+- `process` has many new image analysis functions, brought over from the Nanosurf Surface Analyzer (now NSSA).
+- Figures take their units and labels from the file, can be placed in subplots, and there is a new 3D plot.
+
+### Reading files
+Added:
+- New NHF reader that needs only h5py, for file versions 1.1 and 2.0 to 2.6. Images are identical to those of Nanosurf's
+  reader on versions 1.1, 2.0, 2.3, 2.4 and 2.6.
+- Spectroscopy (`afm.spec`): segments, grid position, other units through the file's calibration, force curves.
+- WaveMode NMA (`afm.nma`): `curve()` gives Z, interaction and force of a pixel; `map()` builds per-pixel maps.
+- `afm.units` holds the unit of every channel. `afm.close()` releases an NHF file; `read` also works in a `with` block.
+- `read(..., measurement=)` picks a measurement of an NHF file.
+
+Fixed:
+- 2.2.4 needed `nanosurf` to be imported but did not declare it, and failed on NHF files with `nanosurf` 2.0.7.
+- NID headers were read as Latin-1, so units and sizes came out as `°` and `3µm`.
+- Duplicate `Wait` segments of older NHF files overwrote each other: the second is now `Wait 2`.
+- A third NID channel of the same name overwrote the second: they are now `Amplitude`, `Amplitude2`, `Amplitude3`.
+- A truncated NID file now says so.
+
+### Processing images
+Added:
+- Leveling: `level_flatten`, `level_poly2d`, `level_lines`, `level_align_rows`, `level_facet`, `level_three_point`,
+  `level_median`, `level_rolling_ball`, `level_shift`.
+- Filters: `filter_basic`, `filter_median`, `filter_gaussian`, `filter_fft`, `filter_notch`.
+- Glitches: `glitch_spikes`, `glitch_lines`, `glitch_auto_lines`, `glitch_scars`, `glitch_step_lines`, `glitch_fill_mask`.
+- Masks, kept per channel: `set_mask` and `mask_threshold`, `mask_otsu`, `mask_watershed`, `mask_outliers`, `mask_scars`,
+  `mask_shape`, `mask_floodfill`, `mask_grow`, `mask_shrink`, `mask_invert`, `mask_clear`, `mask_remove_small`,
+  `mask_fill_holes`. Leveling, filters and statistics can use the mask.
+- Geometry and scale: `geometry_crop`, `geometry_flip`, `geometry_rotate`, `geometry_resample`, `geometry_square_pixels`,
+  `rescale_scale`, `rescale_z_to_reference`, `rescale_xy`.
+- Statistics after ISO 25178: `statistics`, `bearing_curve`, `histogram_fit`, `slope_distributions`.
+- Lines: `line_profile`, `step_heights`, `critical_dimension`, `masked_step_height`, and `profile_roughness` after
+  ISO 21920.
+- Spectra and texture: `psd`, `psd_fit`, `spectrum`, `acf`, `line_functions`, `rms_by_scale`, `lattice`.
+- Grain analysis: `grains`.
+- Two channels: `combine`, `find_shift`.
+- Access: `channels`, `array`, `set_channel`, `size`, `unit`, `origin`, and `apply` and `operations`.
+
+Fixed:
+- `NSFopen.process` could not be imported, because `colormaps.py` imported itself.
+- `flatten(inplace=False)` and similar calls changed the data as well as returning the result.
+- `plane_level` was wrong on non-square images.
+- The physical sizes of non-square NHF images were swapped.
+
+### Figures
+Added:
+- `plot3d`, a 3D view after the Surface Analyzer's, with materials, lighting and overlays of another channel. It needs no
+  graphics card.
+- `plot_profile`, `plot_psd`, `plot_histogram_fit`, `plot_bearing`, `plot_acf`.
+- `ax=` to draw into subplots, and `figsize`, `dpi`, `theme` and `color_range` on the plots.
+- `image(profile=)` shows where a line cut lies.
+- Color maps by name, including the Gwyddion gradients now included with the package: `cmap='Gold'`.
+
+Fixed:
+- The default scale bar had zero length on scans of about 2.5 µm or less, and non-integer lengths were labelled wrongly.
+- `hist(color=)` raised an error.
+
+### Changes that can affect existing scripts
+| What | 2.2.4 | 2.3.0 |
+|---|---|---|
+| NHF force curves `[row, col]` | Position in the file | True grid position, row 0 at the bottom |
+| NHF force curves | Arrays | Read on access; `np.asarray(curves)` gives the array |
+| `image` and `hist`, `scale` | `1e9` for every channel | A readable unit from the channel; `scale=1e9` still forces it |
+| `hist`, `xlabel` | `Z-Axis [nm]` for every channel | The channel and its unit |
+| `image`, color bar | Only with `cbar=` | Always; `colorbar=False` turns it off |
+| `image`, pixels | matplotlib's default | `interpolation='nearest'`; can be overridden |
+| `remove_outliers` | Nearest neighbors with scikit-learn | Interpolation from the pixels around; the numbers differ, and `neighbors` is gone |
+| Unknown channel | pandas `KeyError` | `ValueError` that lists the channels |
+| Default channel | `Z-Axis` only | Falls back to `Topography` in files that have no `Z-Axis` |
+| `NSFopen.read.checkFileType` | Present | Removed |
+
+`stats()` keeps its results, including `Sku` as excess kurtosis (0 for a Gaussian surface). The new `statistics()` gives
+the ISO value of `Sku` (3 for a Gaussian surface).
+
+### Examples
+- All are rewritten around `process`, and there is a new `Grain_Analysis`.
+- **`Spring_Constant`: the result changes from 14.5 to 24.0 N/m.** The old fit used a power formula on amplitude data and
+  found Q = 253; the file records Nanosurf's own Q of 442, and the corrected fit finds 417.
+- `Plotting_Data`: the image was drawn upside down.
+- `Force_Spectroscopy`: the map axes were labelled µm but showed pixels.
+- `Sharpen_Image`: it no longer passes the data through an 8-bit JPEG, and needs neither OpenCV nor PIL.
+- `Plane_Removal`: it crashed on non-square images, and its clipping changed the data.
+- `Lateral_Force`: the offset between the scans is measured instead of set by hand.
+- Renamed without spaces: `Plotting_Data.py`, `Lateral_Force_Processing.py`, `Sharpen_Image.py`.
+
+### Requirements
+- matplotlib 3.6 or newer; the other requirements are unchanged (numpy, scipy, pandas, h5py, Python 3.9 or newer).
+- Removed: `nanosurf` and `scikit-learn`, which 2.2.4 used without declaring them.
+
+## Earlier versions
+The earlier releases have no change notes. Their list and dates are on
+[PyPI](https://pypi.org/project/NSFopen/#history).

nsfopen-2.4.1/NSFopen/_version.py

@@ -0,0 +1 @@
+__version__ = "2.4.1"

{nsfopen-2.4.0 → nsfopen-2.4.1}/NSFopen/read/read.py

@@ -524,7 +524,7 @@ class nid_read:
         if self.__dataframe:
             # import pandas as pd
             self.data = toPandaDF(dataout).unstack(level=0)
-            self.data.dropna(inplace=True)
+            self.data = self.data.dropna()          # not inplace=True: deprecated from pandas 3.1 (PDEP-8)
             # self.specunits = pd.DataFrame(specUnits)
             self.param = toPandaSeries(parameters)
         else:

{nsfopen-2.4.0 → nsfopen-2.4.1/NSFopen.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NSFopen
-Version: 2.4.0
+Version: 2.4.1
 Summary: Python module to open and analyze Nanosurf NID and NHF files
 Author: Nanosurf AG
 Author-email: scripting@nanosurf.com
@@ -30,6 +30,9 @@ Dynamic: summary
 # NSFopen
 Open and analyze Nanosurf NID and NHF files in Python: images, force spectroscopy and WaveMode NMA.
 
+## What's new in 2.4.1
+A fix: reading NID files no longer gives a pandas warning (pandas 3.1 and newer).
+
 ## What's new in 2.4.0
 Compared to 2.3.0:
 - **Force curve analysis:** `process.spectroscopy` and `process.contact` fit force curves and force maps with Hertz,

{nsfopen-2.4.0/NSFopen.egg-info → nsfopen-2.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NSFopen
-Version: 2.4.0
+Version: 2.4.1
 Summary: Python module to open and analyze Nanosurf NID and NHF files
 Author: Nanosurf AG
 Author-email: scripting@nanosurf.com
@@ -30,6 +30,9 @@ Dynamic: summary
 # NSFopen
 Open and analyze Nanosurf NID and NHF files in Python: images, force spectroscopy and WaveMode NMA.
 
+## What's new in 2.4.1
+A fix: reading NID files no longer gives a pandas warning (pandas 3.1 and newer).
+
 ## What's new in 2.4.0
 Compared to 2.3.0:
 - **Force curve analysis:** `process.spectroscopy` and `process.contact` fit force curves and force maps with Hertz,

{nsfopen-2.4.0 → nsfopen-2.4.1}/README.md

@@ -1,175 +1,178 @@
-# NSFopen
-Open and analyze Nanosurf NID and NHF files in Python: images, force spectroscopy and WaveMode NMA.
-
-## What's new in 2.4.0
-Compared to 2.3.0:
-- **Force curve analysis:** `process.spectroscopy` and `process.contact` fit force curves and force maps with Hertz,
-  Sneddon, DMT, JKR and Oliver-Pharr for sphere, cone, pyramid, flat punch and hyperboloid tips, with baseline and
-  interference removal, statistics, maps and CSV; `process.iv` analyzes I-V curves. The same calculations as the
-  Spectroscopy page of NSSA (NSF Surface and Spectroscopy Analyzer).
-- **Color maps of its own:** 12 named maps (`Sky`, `Warm`, `Flare`, ...) defined in the code; `register()` makes them
-  usable by name in matplotlib. The Gwyddion gradient files are no longer included, but an installed Gwyddion's are
-  found on Windows, macOS and Linux.
-
-## What's new in 2.3.0
-Compared to 2.2.4:
-- **Works by itself:** the `nanosurf` and `scikit-learn` packages are no longer needed.
-- **NHF spectroscopy and WaveMode NMA:** files of any size open immediately, and curves are read when asked for.
-- **Image analysis from NSSA (then called Nanosurf Surface Analyzer):** leveling, filters, masks, ISO statistics, line
-  cuts, step heights, critical dimension, PSD fits, lattice and grains.
-- **Better figures:** units and labels from the file, subplots with `ax=`, a new 3D plot, and plots of the analysis results.
-- **Examples rewritten,** with several bugs fixed. The `Spring_Constant` result changes from 14.5 to 24.0 N/m, because the
-  old fit used the wrong formula.
-
-Some defaults changed, which can affect existing scripts:
-- NHF force curves `[row, col]` now give the true grid position.
-- `image` and `hist` choose their unit from the channel; `scale=1e9` still forces nm.
-- `image` shows a color bar unless `colorbar=False`.
-- `remove_outliers` gives different numbers and no longer takes `neighbors`.
-
-`CHANGELOG.md`, in the source distribution, has the full list.
-
-## Installing
-From PyPi
-```
-pip install NSFopen
-```
-
-Needs numpy, scipy, pandas, h5py and matplotlib 3.6 or newer. Examples are in the example folder; `NSFopen_help` shows where. Each
-is a notebook with its `.py` and `.html`, to run from its own folder:
-
-| Example | Shows |
-|---|---|
-| `Plotting_Data` | Leveling with a mask, figures for a report, subplots, 3D |
-| `Calculate_Roughness` | Surface statistics, height distribution, bearing curve, PSD, roughness along a line |
-| `Plane_Removal` | Leveling all the files of a folder |
-| `Grain_Analysis` | Finding features and measuring each of them |
-| `Lateral_Force` | Friction from the forward and backward scans |
-| `Force_Spectroscopy` | Fitting a force map with the DMT model; `Contact_Models.py`: the same with `process.spectroscopy`, maps and the quality filter |
-| `Spring_Constant` | Sader method from a thermal tune |
-| `Sharpen_Image` | Your own processing on the arrays, stored back as channels |
-
-## Reading files
-```python
-from NSFopen.read import read
-
-afm = read('filename.nid')  # or .nhf
-afm.data['Image']['Forward']['Z-Axis']  # an image, in SI units
-afm.param                               # parameters of the file
-afm.units[('Image', 'Forward', 'Z-Axis')]
-```
-Row 0 of an image is the first line scanned, which is the bottom of the picture for an upward scan.
-
-### Spectroscopy (.nhf)
-Files of any size open immediately: curves are read when you ask for them.
-```python
-afm = read('grid.nhf')
-afm.spec.segments, afm.spec.shape, afm.spec.n_points
-
-deflection = afm.spec['Retract 1']['Deflection']
-deflection[10]        # 11th curve in acquisition order
-deflection[2, 3]      # curve at row 2, column 3 of the grid, row 0 at the bottom
-deflection.to('m')[2, 3]   # in another unit, if the file holds its calibration
-deflection.curves()   # all curves, which may differ in length
-deflection.array()    # all curves as (rows, columns, samples), padded with NaN
-
-z, force = afm.spec.force_curve('Retract 1', (2, 3))
-afm.close()
-```
-`afm.data['Spec']['Retract 1']['Deflection']` is the same object.
-
-### WaveMode NMA (.nhf)
-The scalar channels are in `afm.data` as for any image, the per-pixel curves in `afm.nma`.
-```python
-afm = read('nma.nhf')
-curve = afm.nma.curve((100, 200), scan='Forward')  # row, column
-curve.z, curve.interaction, curve.force
-z_advance, force_advance = curve.advance
-z_retract, force_retract = curve.retract
-
-adhesion = afm.nma.map()  # most negative interaction of every pixel, in V
-stiff = afm.nma.map(lambda block: block.max(axis=1), scan='Backward')  # any function of (pixels, samples)
-```
-
-## Processing images
-```python
-from NSFopen.process import process
-
-afm = process('filename.nhf')
-afm.level_flatten()                     # align the lines, then subtract a plane
-afm.mask_otsu()                         # two-level image: mask the upper level
-afm.flatten(fit_on='exclude')           # level the lines on what is not masked
-
-afm.statistics(region='unmasked')       # Sa, Sq, Ssk, Sku, Sdq, Sdr, Sal, Str, ... with units
-grains = afm.grains(split='height')     # one row per grain in grains.table
-profile = afm.line_profile((0, 1e-6), (2e-6, 1e-6), width=5)   # end points in m
-afm.step_heights(profile).steps
-afm.critical_dimension(profile).features
-afm.profile_roughness(profile).params   # ISO 21920
-afm.psd_fit().summary()                 # corner, power law, noise floor, resolution
-afm.lattice().summary()
-
-afm.image(show_mask=True)
-afm.hist()
-afm.plot3d()                            # 3D, colored by height
-afm.plot3d(material='Gold', tilt=60)    # 3D, a material under a light
-afm.plot3d(color='Phase')               # 3D, colored by another channel
-```
-`afm.array()` gives a channel as an array and `afm.set_channel(values, channel='Name', unit='m')` stores your own array
-as a channel, for all the functions below.
-
-All processing works on one channel, by default `direction='Forward'` and the height, which files call `Z-Axis` or
-`Topography`; `afm.channels` lists them all. It changes the channel unless `inplace=False`, when the new array is
-returned instead.
-
-| Group | Methods |
-|---|---|
-| Leveling | `flatten`, `plane_level`, `level_flatten`, `level_poly2d`, `level_lines`, `level_align_rows`, `level_facet`, `level_three_point`, `level_median`, `level_rolling_ball`, `level_shift` |
-| Filters | `denoise`, `filter_basic`, `filter_median`, `filter_gaussian`, `filter_fft`, `filter_notch` |
-| Glitches | `remove_outliers`, `glitch_spikes`, `glitch_lines`, `glitch_auto_lines`, `glitch_scars`, `glitch_step_lines`, `glitch_fill_mask` |
-| Masks | `set_mask`, `mask_threshold`, `mask_otsu`, `mask_watershed`, `mask_outliers`, `mask_scars`, `mask_shape`, `mask_floodfill`, `mask_grow`, `mask_shrink`, `mask_invert`, `mask_clear`, `mask_remove_small`, `mask_fill_holes` |
-| Geometry and scale | `geometry_crop`, `geometry_flip`, `geometry_rotate`, `geometry_resample`, `geometry_square_pixels`, `rescale_scale`, `rescale_z_to_reference`, `rescale_xy` |
-| Height statistics | `stats`, `statistics`, `bearing_curve`, `histogram_fit`, `slope_distributions` |
-| Lines | `line_profile`, `step_heights`, `critical_dimension`, `profile_roughness`, `masked_step_height` |
-| Spectra and texture | `psd`, `psd_fit`, `spectrum`, `acf`, `line_functions`, `rms_by_scale`, `lattice` |
-| Grains | `grains` |
-| Two channels | `combine`, `find_shift` |
-| Plots | `image`, `thumb`, `hist`, `plot3d`, `plot_profile`, `plot_psd`, `plot_histogram_fit`, `plot_bearing`, `plot_acf` |
-
-`help(process.level_rolling_ball)` explains a method and its parameters; `process.operations()` lists the operations
-with their defaults.
-
-## Figures
-`image`, `hist`, `thumb` and `plot3d` take a channel and return a matplotlib figure, with the unit (nm, mV, ...) and
-labels from the file.
-```python
-fig = afm.image(channel='Phase', color_range='p1', cmap='viridis')   # color range: 'full', 'p1' (1-99 %) or (low, high)
-fig.savefig('phase.png')
-
-afm.image(scalebar=True, title=None, figsize=(4, 4), dpi=600, theme='dark')
-
-import matplotlib.pyplot as plt
-fig, axes = plt.subplots(1, 3, figsize=(12, 4), layout='constrained')
-afm.image(ax=axes[0])
-afm.hist(ax=axes[1])
-afm.plot3d(material='Gold', ax=axes[2])
-```
-
-Results of the analysis have their plots too, with the same options:
-```python
-profile = afm.line_profile((0, 1e-6), (2e-6, 1e-6), width=5)
-afm.image(profile=profile)              # where the line is
-afm.plot_profile(profile, steps=afm.step_heights(profile))   # or cd=afm.critical_dimension(profile)
-afm.plot_psd()                          # with a fit; fit=None for the data alone
-afm.plot_histogram_fit(model='gauss2')
-afm.plot_bearing()
-afm.plot_acf()
-```
-
-## Color maps
-```python
-from NSFopen.process import colors
-afm.image(cmap='Gold')           # by name
-afm.image(cmap=colors('Gold').cmap)
-```
-The Gwyddion gradients are included with the package.
+# NSFopen
+Open and analyze Nanosurf NID and NHF files in Python: images, force spectroscopy and WaveMode NMA.
+
+## What's new in 2.4.1
+A fix: reading NID files no longer gives a pandas warning (pandas 3.1 and newer).
+
+## What's new in 2.4.0
+Compared to 2.3.0:
+- **Force curve analysis:** `process.spectroscopy` and `process.contact` fit force curves and force maps with Hertz,
+  Sneddon, DMT, JKR and Oliver-Pharr for sphere, cone, pyramid, flat punch and hyperboloid tips, with baseline and
+  interference removal, statistics, maps and CSV; `process.iv` analyzes I-V curves. The same calculations as the
+  Spectroscopy page of NSSA (NSF Surface and Spectroscopy Analyzer).
+- **Color maps of its own:** 12 named maps (`Sky`, `Warm`, `Flare`, ...) defined in the code; `register()` makes them
+  usable by name in matplotlib. The Gwyddion gradient files are no longer included, but an installed Gwyddion's are
+  found on Windows, macOS and Linux.
+
+## What's new in 2.3.0
+Compared to 2.2.4:
+- **Works by itself:** the `nanosurf` and `scikit-learn` packages are no longer needed.
+- **NHF spectroscopy and WaveMode NMA:** files of any size open immediately, and curves are read when asked for.
+- **Image analysis from NSSA (then called Nanosurf Surface Analyzer):** leveling, filters, masks, ISO statistics, line
+  cuts, step heights, critical dimension, PSD fits, lattice and grains.
+- **Better figures:** units and labels from the file, subplots with `ax=`, a new 3D plot, and plots of the analysis results.
+- **Examples rewritten,** with several bugs fixed. The `Spring_Constant` result changes from 14.5 to 24.0 N/m, because the
+  old fit used the wrong formula.
+
+Some defaults changed, which can affect existing scripts:
+- NHF force curves `[row, col]` now give the true grid position.
+- `image` and `hist` choose their unit from the channel; `scale=1e9` still forces nm.
+- `image` shows a color bar unless `colorbar=False`.
+- `remove_outliers` gives different numbers and no longer takes `neighbors`.
+
+`CHANGELOG.md`, in the source distribution, has the full list.
+
+## Installing
+From PyPi
+```
+pip install NSFopen
+```
+
+Needs numpy, scipy, pandas, h5py and matplotlib 3.6 or newer. Examples are in the example folder; `NSFopen_help` shows where. Each
+is a notebook with its `.py` and `.html`, to run from its own folder:
+
+| Example | Shows |
+|---|---|
+| `Plotting_Data` | Leveling with a mask, figures for a report, subplots, 3D |
+| `Calculate_Roughness` | Surface statistics, height distribution, bearing curve, PSD, roughness along a line |
+| `Plane_Removal` | Leveling all the files of a folder |
+| `Grain_Analysis` | Finding features and measuring each of them |
+| `Lateral_Force` | Friction from the forward and backward scans |
+| `Force_Spectroscopy` | Fitting a force map with the DMT model; `Contact_Models.py`: the same with `process.spectroscopy`, maps and the quality filter |
+| `Spring_Constant` | Sader method from a thermal tune |
+| `Sharpen_Image` | Your own processing on the arrays, stored back as channels |
+
+## Reading files
+```python
+from NSFopen.read import read
+
+afm = read('filename.nid')  # or .nhf
+afm.data['Image']['Forward']['Z-Axis']  # an image, in SI units
+afm.param                               # parameters of the file
+afm.units[('Image', 'Forward', 'Z-Axis')]
+```
+Row 0 of an image is the first line scanned, which is the bottom of the picture for an upward scan.
+
+### Spectroscopy (.nhf)
+Files of any size open immediately: curves are read when you ask for them.
+```python
+afm = read('grid.nhf')
+afm.spec.segments, afm.spec.shape, afm.spec.n_points
+
+deflection = afm.spec['Retract 1']['Deflection']
+deflection[10]        # 11th curve in acquisition order
+deflection[2, 3]      # curve at row 2, column 3 of the grid, row 0 at the bottom
+deflection.to('m')[2, 3]   # in another unit, if the file holds its calibration
+deflection.curves()   # all curves, which may differ in length
+deflection.array()    # all curves as (rows, columns, samples), padded with NaN
+
+z, force = afm.spec.force_curve('Retract 1', (2, 3))
+afm.close()
+```
+`afm.data['Spec']['Retract 1']['Deflection']` is the same object.
+
+### WaveMode NMA (.nhf)
+The scalar channels are in `afm.data` as for any image, the per-pixel curves in `afm.nma`.
+```python
+afm = read('nma.nhf')
+curve = afm.nma.curve((100, 200), scan='Forward')  # row, column
+curve.z, curve.interaction, curve.force
+z_advance, force_advance = curve.advance
+z_retract, force_retract = curve.retract
+
+adhesion = afm.nma.map()  # most negative interaction of every pixel, in V
+stiff = afm.nma.map(lambda block: block.max(axis=1), scan='Backward')  # any function of (pixels, samples)
+```
+
+## Processing images
+```python
+from NSFopen.process import process
+
+afm = process('filename.nhf')
+afm.level_flatten()                     # align the lines, then subtract a plane
+afm.mask_otsu()                         # two-level image: mask the upper level
+afm.flatten(fit_on='exclude')           # level the lines on what is not masked
+
+afm.statistics(region='unmasked')       # Sa, Sq, Ssk, Sku, Sdq, Sdr, Sal, Str, ... with units
+grains = afm.grains(split='height')     # one row per grain in grains.table
+profile = afm.line_profile((0, 1e-6), (2e-6, 1e-6), width=5)   # end points in m
+afm.step_heights(profile).steps
+afm.critical_dimension(profile).features
+afm.profile_roughness(profile).params   # ISO 21920
+afm.psd_fit().summary()                 # corner, power law, noise floor, resolution
+afm.lattice().summary()
+
+afm.image(show_mask=True)
+afm.hist()
+afm.plot3d()                            # 3D, colored by height
+afm.plot3d(material='Gold', tilt=60)    # 3D, a material under a light
+afm.plot3d(color='Phase')               # 3D, colored by another channel
+```
+`afm.array()` gives a channel as an array and `afm.set_channel(values, channel='Name', unit='m')` stores your own array
+as a channel, for all the functions below.
+
+All processing works on one channel, by default `direction='Forward'` and the height, which files call `Z-Axis` or
+`Topography`; `afm.channels` lists them all. It changes the channel unless `inplace=False`, when the new array is
+returned instead.
+
+| Group | Methods |
+|---|---|
+| Leveling | `flatten`, `plane_level`, `level_flatten`, `level_poly2d`, `level_lines`, `level_align_rows`, `level_facet`, `level_three_point`, `level_median`, `level_rolling_ball`, `level_shift` |
+| Filters | `denoise`, `filter_basic`, `filter_median`, `filter_gaussian`, `filter_fft`, `filter_notch` |
+| Glitches | `remove_outliers`, `glitch_spikes`, `glitch_lines`, `glitch_auto_lines`, `glitch_scars`, `glitch_step_lines`, `glitch_fill_mask` |
+| Masks | `set_mask`, `mask_threshold`, `mask_otsu`, `mask_watershed`, `mask_outliers`, `mask_scars`, `mask_shape`, `mask_floodfill`, `mask_grow`, `mask_shrink`, `mask_invert`, `mask_clear`, `mask_remove_small`, `mask_fill_holes` |
+| Geometry and scale | `geometry_crop`, `geometry_flip`, `geometry_rotate`, `geometry_resample`, `geometry_square_pixels`, `rescale_scale`, `rescale_z_to_reference`, `rescale_xy` |
+| Height statistics | `stats`, `statistics`, `bearing_curve`, `histogram_fit`, `slope_distributions` |
+| Lines | `line_profile`, `step_heights`, `critical_dimension`, `profile_roughness`, `masked_step_height` |
+| Spectra and texture | `psd`, `psd_fit`, `spectrum`, `acf`, `line_functions`, `rms_by_scale`, `lattice` |
+| Grains | `grains` |
+| Two channels | `combine`, `find_shift` |
+| Plots | `image`, `thumb`, `hist`, `plot3d`, `plot_profile`, `plot_psd`, `plot_histogram_fit`, `plot_bearing`, `plot_acf` |
+
+`help(process.level_rolling_ball)` explains a method and its parameters; `process.operations()` lists the operations
+with their defaults.
+
+## Figures
+`image`, `hist`, `thumb` and `plot3d` take a channel and return a matplotlib figure, with the unit (nm, mV, ...) and
+labels from the file.
+```python
+fig = afm.image(channel='Phase', color_range='p1', cmap='viridis')   # color range: 'full', 'p1' (1-99 %) or (low, high)
+fig.savefig('phase.png')
+
+afm.image(scalebar=True, title=None, figsize=(4, 4), dpi=600, theme='dark')
+
+import matplotlib.pyplot as plt
+fig, axes = plt.subplots(1, 3, figsize=(12, 4), layout='constrained')
+afm.image(ax=axes[0])
+afm.hist(ax=axes[1])
+afm.plot3d(material='Gold', ax=axes[2])
+```
+
+Results of the analysis have their plots too, with the same options:
+```python
+profile = afm.line_profile((0, 1e-6), (2e-6, 1e-6), width=5)
+afm.image(profile=profile)              # where the line is
+afm.plot_profile(profile, steps=afm.step_heights(profile))   # or cd=afm.critical_dimension(profile)
+afm.plot_psd()                          # with a fit; fit=None for the data alone
+afm.plot_histogram_fit(model='gauss2')
+afm.plot_bearing()
+afm.plot_acf()
+```
+
+## Color maps
+```python
+from NSFopen.process import colors
+afm.image(cmap='Gold')           # by name
+afm.image(cmap=colors('Gold').cmap)
+```
+The Gwyddion gradients are included with the package.

nsfopen-2.4.0/NSFopen/_version.py

@@ -1 +0,0 @@
-__version__ = "2.4.0"