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| author | CoprDistGit <infra@openeuler.org> | 2023-05-18 03:28:27 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-18 03:28:27 +0000 |
| commit | 6361db8d8d4689f4ef61cd24818dde02d459eb65 (patch) | |
| tree | b062370a3a871359928a7b4992fec59550c2d3be | |
| parent | 875cd4f885655f2aecaa084ee4ed361da1529daa (diff) | |
automatic import of python-renishawwire
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-renishawwire.spec | 955 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 957 insertions, 0 deletions
@@ -0,0 +1 @@ +/renishawWiRE-0.1.16.tar.gz diff --git a/python-renishawwire.spec b/python-renishawwire.spec new file mode 100644 index 0000000..4cfcc67 --- /dev/null +++ b/python-renishawwire.spec @@ -0,0 +1,955 @@ +%global _empty_manifest_terminate_build 0 +Name: python-renishawWiRE +Version: 0.1.16 +Release: 1 +Summary: Reading wdf Raman spectroscopy file from Renishaw WiRE +License: MIT +URL: https://github.com/alchem0x2A/py-wdf-reader +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/9b/a2/ae5940b9b1b286a06a0f6d6372d0a825d9311c5be4552d053f3cbb543c11/renishawWiRE-0.1.16.tar.gz +BuildArch: noarch + +Requires: python3-numpy +Requires: python3-Pillow +Requires: python3-Pillow +Requires: python3-matplotlib + +%description +# `renishawWiRE` Renishaw Raman spectroscopy parser in python + +[](https://badge.fury.io/py/renishawWiRE) +[](https://anaconda.org/conda-forge/renishaw_wire) + + + +A python wrapper for read-only accessing the wdf Raman spectroscopy file format created +by the WiRE software of Ranishaw Inc. Renishaw Inc owns copyright of +the wdf file format. + +Ideas for reverse-engineering the WDF format is inspired by: + +- [Renishaw File Reader](https://zenodo.org/record/495477#.XsZs3y17FBw) by Alex Henderson (DOI:10.5281/zenodo.495477)) +- Renishaw IO module in [`Gwyddion`](http://gwyddion.net/module-list-nocss.en.php) + +# Installation + +Requirements: + +- `python>=3.6` +- `Numpy>=1.12.0` +- `Matplotlib>=2.1.0` (optional, if you want to plot the spectra in the examples) +- `Pillow>=3.4.0` (optional, if you want to extract the white light + image) + + **Warning** there are some API changes to `Pillow` after + version 7.2.0 (thanks @markotoplak). Please update `renishawWiRE` + to version >= 0.1.8 if you are experiencing problems with Tiff image + extraction. + +You can choose any of the following installation methods: + +### 1. Versions hosted on PyPI: via `pip` + +```bash +# Optionally on a virtualenv +# Add --user if you don't want to install as sys admin +pip install --upgrade renishawWiRE +``` + +If you need full plotting / image extraction support, consider +specifying the extras to `pip`. +```bash +# Optionally on a virtualenv +pip install --upgrade "renishawWiRE[plot]" +``` + +### 2. `HEAD` version: via `git` + `pip` + +To install the package without examples, run the following commands +(installing extra `matplotlib` and `Pillow` if not present): + +```bash +git clone https://github.com/alchem0x2A/py-wdf-reader.git +cd py-wdf-reader +pip install -e ".[plot]" +``` + +### 3. Via `conda-forge` +The version hosted on `conda-forge` will install all dependent packages including `numpy` `matplotlib` and `Pillow`. +Note the slight difference of package name compared with PyPI. + +```bash +conda install -c conda-forge renishaw_wire +``` + +## Test installation + +Simply try if importing works: +```bash +python -c "import renishawWiRE" +``` +and test the executable binary: +```bash +wdf-export -h +``` + +Additionally, if you want to test the examples, download them from the +[binary +release](https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip) +and overwrite the dummy files within `examples/spectra_files/`: +```bash +wget https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip +unzip -o spectra_files.zip -d examples/ +rm spectra_files.zip +# To avoid unexpected pushing to repo due to large file size +git update-index --skip-worktree examples/spectra_files.wdf +``` + +# Basic Usage + +Check the sample codes in `examples/` folder for more details about +what the package can do. + +## 1. Simple script for exporting wdf spectra (version > 0.1.11) + +The package also installs a simple wrapper script `wdf-export` for +exporting spectra in the wdf file to plain-text formats. If the +measurement contains mapping information, the optical image is also +exported (as `.svg` file) + +### Usage +Simply use the base name of input file for the exported text file: +```bash +wdf-export path/to/wdf_file +``` +or specifying the input and output files +```bash +wdf-export path/to/wdf_file -o path/to/output.csv +``` + + + + +## 2. Python API +### Get file information + +`renishawWiRE.WDFReader` is the main entry point to get information of a WDF file. + +```python +# The following example shows how to get the info from a WDF file +# Check `examples/ex1_getinfo.py` +from renishawWiRE import WDFReader + +#`filename` can be string, file obj or `pathlib.Path` +filename = "path/to/your/file.wdf" +reader = WDFReader(filename) +reader.print_info() +``` + +### Get single point spectrum / spectra + +When the spectrum is single-point (`WDFReader.measurement_type == 1`), +`WDFReader.xdata` is the spectral points, and `WDFReader.spectra` is +the accumulated spectrum. + +```python +# Example to read and plot single point spectrum +# Assume same file as in previous section +# Check `examples/ex2_sp_spectra.py` +import matplotlib.pyplot as plt +wavenumber = reader.xdata +spectra = reader.spectra +plt.plot(wavenumber, spectra) +``` + +An [example](examples/ex2_sp_spectra.py) is shown below: + + + +### Get depth series spectra + +A depth series measures contains single point spectra with varied +Z-depth. For this type `WDFReader.measurement_type == 2`. The code to +get the spectra are the same as the one in the single point spectra +measurement, instead that the `WDFReade.spectra` becomes a matrix with +size of `(count, point_per_spectrum)`. The `WDFReader.zpos` returns +the values of z-scan points. + +For details of Z-depth data processing, check this +[example](examples/ex8_depth.py) + + + + + + + + +### Get line scan from StreamLine™ / StreamHR Line™ measurements + +For mapped measurements (line or grid scan), +`WDFReader.measurement_type == 3`. The code to get the spectra are +the same as the one in the single point spectra measurement, instead +that the `WDFReade.spectra` becomes a matrix with size of `(count, point_per_spectrum)`: + +```python +# Example to read line scane spectrum +# Check `examples/ex3_linscan.py` +filename = "path/to/line-scan.wdf" +reader = WDFReader(filename) +wn = reader.xdata +spectra = reader.spectra +print(wn.shape, spectra.shape) +``` + +An [example](examples/ex3_linscan.py) of the line scane is shown below: + + + +It is also possible to correlate the xy-coordinates with the +spectra. For a mapping measurement, `WDFReader.xpos` and +`WDFReader.ypos` will contain the point-wise x and y coordinates. + +```python +# Check examples/ex4_linxy.py for details +x = reader.xpos +y = reader.ypos +# Cartesian distance +d = (x ** 2 + y ** 2) ** (1 / 2) +``` + + +### Get grid mapping from StreamLine™ / StreamHR Line™ measurements + +Finally let's extract the grid-spaced Raman data. For mapping data +with `spectra_w` pixels in the x-direction and `spectra_h` in the +y-direction, the matrix of spectra is shaped into `(spectra_h, +spectra_w, points_per_spectrum)`. + +Make sure your xy-coordinates starts from the top left corner. + +```python +# For gridded data, x and y are on rectangle grids +# check examples/ex5_mapping.py for details +x = reader.xpos +y = reader.ypos +spectra = reader.spectra +# Use other packages to handle spectra +# write yourself the function or use a 3rd-party libray +mapped_data = some_treating_function(spectra, **params) +# plot mapped data using plt.imshow +plt.pcolor(mapped_data, extends=[0, x.max() - x.min(), + y.max() - y.min(), 0]) +``` +An [example](examples/ex5_mapping.py) of mapping data is shown below: + + + +You can also work on the white-light image which automatically saved +during a mapped scan. The jpeg-form image can be obtained by +`WDFReader.img` as an io object, and some further informations about +the dimensions etc. For this to work you need `Pillow` installed as third-party +library: + +- Get coordinates of white-light image + +```python +# There are two-sets of coordinates. +# `xpos` and `ypos` are the Stage XY-coordinate of the mapped area +# while `img_origins` and `img_dimensions` are size (μm) of white-light image +# See examples/ex6_mapping_img.py for details +import matplotlib.image as mpimg +img_x0, img_y0 = reader.img_origins +img_w, img_h = reader.img_dimensions +plt.imshow(reader.img, + extent=(img_x0, img_x0 + img_w, + img_y0 + img_h, img_y0)) +``` +An [example](examples/ex6_mapping_img.py) of mapped area on white light image is shown below: + + + +- Overlaying white-light image with mapped spectra + +```python +# `img_cropbox` is the pixel positions for cropping +# Requires PIL to operate +# See examples/ex7_overlay_mapping.py for details +img = PIL.Image.open(reader.img) +img1 = img.crop(box=reader.img_cropbox) +extent = ... # Same extent for both images +plt.imshow(img1, alpha=0.5, extent=extent) # White light image +plt.imshow(spectra, alpha=0.5, extent=extent) # Mapped spectra +``` + +The following [example](examples/ex7_overlay_mapping.py) shows the +overlayed image of both fields. Some degree of misalignment can be +observed. + + + + + + +# TODOs + +There are still several functionalities not implemented: + +- [x] Extract image info +- [x] Verify image coordinate superposition +- [x] Improve series measurement retrieval +- [ ] Testing on various version of Renishaw instruments +- [x] Binary utilities + +# Bug reports + +The codes are only tested on the Raman spectra files that generated +from my personal measurements. If you encounter any peculiar behavior +of the package please kindly open an issue with your report / +suggestions. Thx! + + + +%package -n python3-renishawWiRE +Summary: Reading wdf Raman spectroscopy file from Renishaw WiRE +Provides: python-renishawWiRE +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-renishawWiRE +# `renishawWiRE` Renishaw Raman spectroscopy parser in python + +[](https://badge.fury.io/py/renishawWiRE) +[](https://anaconda.org/conda-forge/renishaw_wire) + + + +A python wrapper for read-only accessing the wdf Raman spectroscopy file format created +by the WiRE software of Ranishaw Inc. Renishaw Inc owns copyright of +the wdf file format. + +Ideas for reverse-engineering the WDF format is inspired by: + +- [Renishaw File Reader](https://zenodo.org/record/495477#.XsZs3y17FBw) by Alex Henderson (DOI:10.5281/zenodo.495477)) +- Renishaw IO module in [`Gwyddion`](http://gwyddion.net/module-list-nocss.en.php) + +# Installation + +Requirements: + +- `python>=3.6` +- `Numpy>=1.12.0` +- `Matplotlib>=2.1.0` (optional, if you want to plot the spectra in the examples) +- `Pillow>=3.4.0` (optional, if you want to extract the white light + image) + + **Warning** there are some API changes to `Pillow` after + version 7.2.0 (thanks @markotoplak). Please update `renishawWiRE` + to version >= 0.1.8 if you are experiencing problems with Tiff image + extraction. + +You can choose any of the following installation methods: + +### 1. Versions hosted on PyPI: via `pip` + +```bash +# Optionally on a virtualenv +# Add --user if you don't want to install as sys admin +pip install --upgrade renishawWiRE +``` + +If you need full plotting / image extraction support, consider +specifying the extras to `pip`. +```bash +# Optionally on a virtualenv +pip install --upgrade "renishawWiRE[plot]" +``` + +### 2. `HEAD` version: via `git` + `pip` + +To install the package without examples, run the following commands +(installing extra `matplotlib` and `Pillow` if not present): + +```bash +git clone https://github.com/alchem0x2A/py-wdf-reader.git +cd py-wdf-reader +pip install -e ".[plot]" +``` + +### 3. Via `conda-forge` +The version hosted on `conda-forge` will install all dependent packages including `numpy` `matplotlib` and `Pillow`. +Note the slight difference of package name compared with PyPI. + +```bash +conda install -c conda-forge renishaw_wire +``` + +## Test installation + +Simply try if importing works: +```bash +python -c "import renishawWiRE" +``` +and test the executable binary: +```bash +wdf-export -h +``` + +Additionally, if you want to test the examples, download them from the +[binary +release](https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip) +and overwrite the dummy files within `examples/spectra_files/`: +```bash +wget https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip +unzip -o spectra_files.zip -d examples/ +rm spectra_files.zip +# To avoid unexpected pushing to repo due to large file size +git update-index --skip-worktree examples/spectra_files.wdf +``` + +# Basic Usage + +Check the sample codes in `examples/` folder for more details about +what the package can do. + +## 1. Simple script for exporting wdf spectra (version > 0.1.11) + +The package also installs a simple wrapper script `wdf-export` for +exporting spectra in the wdf file to plain-text formats. If the +measurement contains mapping information, the optical image is also +exported (as `.svg` file) + +### Usage +Simply use the base name of input file for the exported text file: +```bash +wdf-export path/to/wdf_file +``` +or specifying the input and output files +```bash +wdf-export path/to/wdf_file -o path/to/output.csv +``` + + + + +## 2. Python API +### Get file information + +`renishawWiRE.WDFReader` is the main entry point to get information of a WDF file. + +```python +# The following example shows how to get the info from a WDF file +# Check `examples/ex1_getinfo.py` +from renishawWiRE import WDFReader + +#`filename` can be string, file obj or `pathlib.Path` +filename = "path/to/your/file.wdf" +reader = WDFReader(filename) +reader.print_info() +``` + +### Get single point spectrum / spectra + +When the spectrum is single-point (`WDFReader.measurement_type == 1`), +`WDFReader.xdata` is the spectral points, and `WDFReader.spectra` is +the accumulated spectrum. + +```python +# Example to read and plot single point spectrum +# Assume same file as in previous section +# Check `examples/ex2_sp_spectra.py` +import matplotlib.pyplot as plt +wavenumber = reader.xdata +spectra = reader.spectra +plt.plot(wavenumber, spectra) +``` + +An [example](examples/ex2_sp_spectra.py) is shown below: + + + +### Get depth series spectra + +A depth series measures contains single point spectra with varied +Z-depth. For this type `WDFReader.measurement_type == 2`. The code to +get the spectra are the same as the one in the single point spectra +measurement, instead that the `WDFReade.spectra` becomes a matrix with +size of `(count, point_per_spectrum)`. The `WDFReader.zpos` returns +the values of z-scan points. + +For details of Z-depth data processing, check this +[example](examples/ex8_depth.py) + + + + + + + + +### Get line scan from StreamLine™ / StreamHR Line™ measurements + +For mapped measurements (line or grid scan), +`WDFReader.measurement_type == 3`. The code to get the spectra are +the same as the one in the single point spectra measurement, instead +that the `WDFReade.spectra` becomes a matrix with size of `(count, point_per_spectrum)`: + +```python +# Example to read line scane spectrum +# Check `examples/ex3_linscan.py` +filename = "path/to/line-scan.wdf" +reader = WDFReader(filename) +wn = reader.xdata +spectra = reader.spectra +print(wn.shape, spectra.shape) +``` + +An [example](examples/ex3_linscan.py) of the line scane is shown below: + + + +It is also possible to correlate the xy-coordinates with the +spectra. For a mapping measurement, `WDFReader.xpos` and +`WDFReader.ypos` will contain the point-wise x and y coordinates. + +```python +# Check examples/ex4_linxy.py for details +x = reader.xpos +y = reader.ypos +# Cartesian distance +d = (x ** 2 + y ** 2) ** (1 / 2) +``` + + +### Get grid mapping from StreamLine™ / StreamHR Line™ measurements + +Finally let's extract the grid-spaced Raman data. For mapping data +with `spectra_w` pixels in the x-direction and `spectra_h` in the +y-direction, the matrix of spectra is shaped into `(spectra_h, +spectra_w, points_per_spectrum)`. + +Make sure your xy-coordinates starts from the top left corner. + +```python +# For gridded data, x and y are on rectangle grids +# check examples/ex5_mapping.py for details +x = reader.xpos +y = reader.ypos +spectra = reader.spectra +# Use other packages to handle spectra +# write yourself the function or use a 3rd-party libray +mapped_data = some_treating_function(spectra, **params) +# plot mapped data using plt.imshow +plt.pcolor(mapped_data, extends=[0, x.max() - x.min(), + y.max() - y.min(), 0]) +``` +An [example](examples/ex5_mapping.py) of mapping data is shown below: + + + +You can also work on the white-light image which automatically saved +during a mapped scan. The jpeg-form image can be obtained by +`WDFReader.img` as an io object, and some further informations about +the dimensions etc. For this to work you need `Pillow` installed as third-party +library: + +- Get coordinates of white-light image + +```python +# There are two-sets of coordinates. +# `xpos` and `ypos` are the Stage XY-coordinate of the mapped area +# while `img_origins` and `img_dimensions` are size (μm) of white-light image +# See examples/ex6_mapping_img.py for details +import matplotlib.image as mpimg +img_x0, img_y0 = reader.img_origins +img_w, img_h = reader.img_dimensions +plt.imshow(reader.img, + extent=(img_x0, img_x0 + img_w, + img_y0 + img_h, img_y0)) +``` +An [example](examples/ex6_mapping_img.py) of mapped area on white light image is shown below: + + + +- Overlaying white-light image with mapped spectra + +```python +# `img_cropbox` is the pixel positions for cropping +# Requires PIL to operate +# See examples/ex7_overlay_mapping.py for details +img = PIL.Image.open(reader.img) +img1 = img.crop(box=reader.img_cropbox) +extent = ... # Same extent for both images +plt.imshow(img1, alpha=0.5, extent=extent) # White light image +plt.imshow(spectra, alpha=0.5, extent=extent) # Mapped spectra +``` + +The following [example](examples/ex7_overlay_mapping.py) shows the +overlayed image of both fields. Some degree of misalignment can be +observed. + + + + + + +# TODOs + +There are still several functionalities not implemented: + +- [x] Extract image info +- [x] Verify image coordinate superposition +- [x] Improve series measurement retrieval +- [ ] Testing on various version of Renishaw instruments +- [x] Binary utilities + +# Bug reports + +The codes are only tested on the Raman spectra files that generated +from my personal measurements. If you encounter any peculiar behavior +of the package please kindly open an issue with your report / +suggestions. Thx! + + + +%package help +Summary: Development documents and examples for renishawWiRE +Provides: python3-renishawWiRE-doc +%description help +# `renishawWiRE` Renishaw Raman spectroscopy parser in python + +[](https://badge.fury.io/py/renishawWiRE) +[](https://anaconda.org/conda-forge/renishaw_wire) + + + +A python wrapper for read-only accessing the wdf Raman spectroscopy file format created +by the WiRE software of Ranishaw Inc. Renishaw Inc owns copyright of +the wdf file format. + +Ideas for reverse-engineering the WDF format is inspired by: + +- [Renishaw File Reader](https://zenodo.org/record/495477#.XsZs3y17FBw) by Alex Henderson (DOI:10.5281/zenodo.495477)) +- Renishaw IO module in [`Gwyddion`](http://gwyddion.net/module-list-nocss.en.php) + +# Installation + +Requirements: + +- `python>=3.6` +- `Numpy>=1.12.0` +- `Matplotlib>=2.1.0` (optional, if you want to plot the spectra in the examples) +- `Pillow>=3.4.0` (optional, if you want to extract the white light + image) + + **Warning** there are some API changes to `Pillow` after + version 7.2.0 (thanks @markotoplak). Please update `renishawWiRE` + to version >= 0.1.8 if you are experiencing problems with Tiff image + extraction. + +You can choose any of the following installation methods: + +### 1. Versions hosted on PyPI: via `pip` + +```bash +# Optionally on a virtualenv +# Add --user if you don't want to install as sys admin +pip install --upgrade renishawWiRE +``` + +If you need full plotting / image extraction support, consider +specifying the extras to `pip`. +```bash +# Optionally on a virtualenv +pip install --upgrade "renishawWiRE[plot]" +``` + +### 2. `HEAD` version: via `git` + `pip` + +To install the package without examples, run the following commands +(installing extra `matplotlib` and `Pillow` if not present): + +```bash +git clone https://github.com/alchem0x2A/py-wdf-reader.git +cd py-wdf-reader +pip install -e ".[plot]" +``` + +### 3. Via `conda-forge` +The version hosted on `conda-forge` will install all dependent packages including `numpy` `matplotlib` and `Pillow`. +Note the slight difference of package name compared with PyPI. + +```bash +conda install -c conda-forge renishaw_wire +``` + +## Test installation + +Simply try if importing works: +```bash +python -c "import renishawWiRE" +``` +and test the executable binary: +```bash +wdf-export -h +``` + +Additionally, if you want to test the examples, download them from the +[binary +release](https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip) +and overwrite the dummy files within `examples/spectra_files/`: +```bash +wget https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip +unzip -o spectra_files.zip -d examples/ +rm spectra_files.zip +# To avoid unexpected pushing to repo due to large file size +git update-index --skip-worktree examples/spectra_files.wdf +``` + +# Basic Usage + +Check the sample codes in `examples/` folder for more details about +what the package can do. + +## 1. Simple script for exporting wdf spectra (version > 0.1.11) + +The package also installs a simple wrapper script `wdf-export` for +exporting spectra in the wdf file to plain-text formats. If the +measurement contains mapping information, the optical image is also +exported (as `.svg` file) + +### Usage +Simply use the base name of input file for the exported text file: +```bash +wdf-export path/to/wdf_file +``` +or specifying the input and output files +```bash +wdf-export path/to/wdf_file -o path/to/output.csv +``` + + + + +## 2. Python API +### Get file information + +`renishawWiRE.WDFReader` is the main entry point to get information of a WDF file. + +```python +# The following example shows how to get the info from a WDF file +# Check `examples/ex1_getinfo.py` +from renishawWiRE import WDFReader + +#`filename` can be string, file obj or `pathlib.Path` +filename = "path/to/your/file.wdf" +reader = WDFReader(filename) +reader.print_info() +``` + +### Get single point spectrum / spectra + +When the spectrum is single-point (`WDFReader.measurement_type == 1`), +`WDFReader.xdata` is the spectral points, and `WDFReader.spectra` is +the accumulated spectrum. + +```python +# Example to read and plot single point spectrum +# Assume same file as in previous section +# Check `examples/ex2_sp_spectra.py` +import matplotlib.pyplot as plt +wavenumber = reader.xdata +spectra = reader.spectra +plt.plot(wavenumber, spectra) +``` + +An [example](examples/ex2_sp_spectra.py) is shown below: + + + +### Get depth series spectra + +A depth series measures contains single point spectra with varied +Z-depth. For this type `WDFReader.measurement_type == 2`. The code to +get the spectra are the same as the one in the single point spectra +measurement, instead that the `WDFReade.spectra` becomes a matrix with +size of `(count, point_per_spectrum)`. The `WDFReader.zpos` returns +the values of z-scan points. + +For details of Z-depth data processing, check this +[example](examples/ex8_depth.py) + + + + + + + + +### Get line scan from StreamLine™ / StreamHR Line™ measurements + +For mapped measurements (line or grid scan), +`WDFReader.measurement_type == 3`. The code to get the spectra are +the same as the one in the single point spectra measurement, instead +that the `WDFReade.spectra` becomes a matrix with size of `(count, point_per_spectrum)`: + +```python +# Example to read line scane spectrum +# Check `examples/ex3_linscan.py` +filename = "path/to/line-scan.wdf" +reader = WDFReader(filename) +wn = reader.xdata +spectra = reader.spectra +print(wn.shape, spectra.shape) +``` + +An [example](examples/ex3_linscan.py) of the line scane is shown below: + + + +It is also possible to correlate the xy-coordinates with the +spectra. For a mapping measurement, `WDFReader.xpos` and +`WDFReader.ypos` will contain the point-wise x and y coordinates. + +```python +# Check examples/ex4_linxy.py for details +x = reader.xpos +y = reader.ypos +# Cartesian distance +d = (x ** 2 + y ** 2) ** (1 / 2) +``` + + +### Get grid mapping from StreamLine™ / StreamHR Line™ measurements + +Finally let's extract the grid-spaced Raman data. For mapping data +with `spectra_w` pixels in the x-direction and `spectra_h` in the +y-direction, the matrix of spectra is shaped into `(spectra_h, +spectra_w, points_per_spectrum)`. + +Make sure your xy-coordinates starts from the top left corner. + +```python +# For gridded data, x and y are on rectangle grids +# check examples/ex5_mapping.py for details +x = reader.xpos +y = reader.ypos +spectra = reader.spectra +# Use other packages to handle spectra +# write yourself the function or use a 3rd-party libray +mapped_data = some_treating_function(spectra, **params) +# plot mapped data using plt.imshow +plt.pcolor(mapped_data, extends=[0, x.max() - x.min(), + y.max() - y.min(), 0]) +``` +An [example](examples/ex5_mapping.py) of mapping data is shown below: + + + +You can also work on the white-light image which automatically saved +during a mapped scan. The jpeg-form image can be obtained by +`WDFReader.img` as an io object, and some further informations about +the dimensions etc. For this to work you need `Pillow` installed as third-party +library: + +- Get coordinates of white-light image + +```python +# There are two-sets of coordinates. +# `xpos` and `ypos` are the Stage XY-coordinate of the mapped area +# while `img_origins` and `img_dimensions` are size (μm) of white-light image +# See examples/ex6_mapping_img.py for details +import matplotlib.image as mpimg +img_x0, img_y0 = reader.img_origins +img_w, img_h = reader.img_dimensions +plt.imshow(reader.img, + extent=(img_x0, img_x0 + img_w, + img_y0 + img_h, img_y0)) +``` +An [example](examples/ex6_mapping_img.py) of mapped area on white light image is shown below: + + + +- Overlaying white-light image with mapped spectra + +```python +# `img_cropbox` is the pixel positions for cropping +# Requires PIL to operate +# See examples/ex7_overlay_mapping.py for details +img = PIL.Image.open(reader.img) +img1 = img.crop(box=reader.img_cropbox) +extent = ... # Same extent for both images +plt.imshow(img1, alpha=0.5, extent=extent) # White light image +plt.imshow(spectra, alpha=0.5, extent=extent) # Mapped spectra +``` + +The following [example](examples/ex7_overlay_mapping.py) shows the +overlayed image of both fields. Some degree of misalignment can be +observed. + + + + + + +# TODOs + +There are still several functionalities not implemented: + +- [x] Extract image info +- [x] Verify image coordinate superposition +- [x] Improve series measurement retrieval +- [ ] Testing on various version of Renishaw instruments +- [x] Binary utilities + +# Bug reports + +The codes are only tested on the Raman spectra files that generated +from my personal measurements. If you encounter any peculiar behavior +of the package please kindly open an issue with your report / +suggestions. Thx! + + + +%prep +%autosetup -n renishawWiRE-0.1.16 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-renishawWiRE -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.16-1 +- Package Spec generated @@ -0,0 +1 @@ +1a3fc42031a97c9abc414a8f6bf84e71 renishawWiRE-0.1.16.tar.gz |