suvtools 1.0.0__tar.gz

suvtools-1.0.0/LICENSE

@@ -0,0 +1,20 @@
+MIT License
+
+Copyright (c) 2020-Present Pranab Das (GitHub: @pranabdas)
+
+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.

suvtools-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: suvtools
+Version: 1.0.0
+Summary: Python library for analyzing and visualizing SSLS SUV Beamline data.
+Home-page: https://pranabdas.github.io/suvtools/
+License: MIT
+Keywords: python,data-analysis,matplotlib,materials-science,surface-science,condensed-matter-physics,photoelectron-spectroscopy,arpes
+Author: Pranab Das
+Requires-Python: >=3.9,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: matplotlib (>=3.9.2,<4.0.0)
+Requires-Dist: numpy (>=2.0.2,<3.0.0)
+Requires-Dist: pandas (>=2.2.3,<3.0.0)
+Requires-Dist: scipy (>=1.13.1,<2.0.0)
+Project-URL: Documentation, https://pranabdas.github.io/suvtools/docs/
+Project-URL: Repository, https://github.com/pranabdas/suvtools
+Description-Content-Type: text/markdown
+
+<h1 align="center">SUV Tools</h1>
+
+<p align="center">
+  <a href="https://github.com/pranabdas/suvtools/actions/workflows/python-tests.yml"><img src="https://github.com/pranabdas/suvtools/actions/workflows/python-tests.yml/badge.svg" alt="Python tests status"></a>
+  <a href="https://github.com/pranabdas/suvtools/actions/workflows/deploy-gh-pages.yml"><img src="https://github.com/pranabdas/suvtools/actions/workflows/deploy-gh-pages.yml/badge.svg" alt="Deploy gh-pages status"></a>
+  <a href="https://github.com/pranabdas/suvtools/blob/master/LICENSE"><img src="https://img.shields.io/github/license/sourcerer-io/hall-of-fame.svg?colorB=A31F34"></a>
+  <a href="https://github.com/pranabdas/suvtools/releases/latest"><img src="https://img.shields.io/github/v/release/pranabdas/suvtools.svg" alt="Latest Release"/></a>
+</p>
+
+
+Visit the project homepage <https://pranabdas.github.io/suvtools/>
+
+## Quick start
+
+Install latest stable release:
+```console
+pip3 install --upgrade suvtools
+```
+
+Import suvtools into your project:
+```python
+import suvtools as suv
+```
+
+**Modules:**
+
+- `suv.load("datafile.txt", scan=None)`: It will return a two dimensional array
+with columns for various parameters. If the second argument, i.e., the scan
+number is not specified, the code will read the last scan from the file.
+
+- `suv.fit_gauss(x, y, a=None, x0=None, sigma=None, xmin=None, xmax=None, num=1000)`:
+returns x, Gaussian fitted y values, and prints out relevant parameters. `xmin`
+and `xmax` determines the range to fit. If `xmin` and `xmax` are not provided,
+whole range is used. `num` determines the number of points returned in `x_fit`
+and `y_fit`.
+
+- `suv.fit_lorentz(x, y, a=None, x0=None, gamma=None, xmin=None, xmax=None, num=1000)`:
+returns x, Lorentzian fitted y values, and prints out relevant parameters.
+`xmin` and `xmax` determines the range to fit. If `xmin` and `xmax` are not
+provided, whole range is used. `num` determines the number of points returned in
+`x_fit` and `y_fit`.
+
+- `suv.save_csv("datafile.txt", csvname=None, scan=None)`: saves scan to a csv
+file. The file will be saved in the save directory as `datafile` with name
+`datafile.csv` unless  `csvname` is specified. Like the `load` module, if the
+scan number is not specified, it will read the last scan from the file.
+
+- `suv.norm_bg(energy, intensity, x1, x2, x_norm_loc=None)`:
+Removes linear background, and normalizes the data. x1, x2 are energy values
+that determines the slope of the background. By default the normalization done
+at the tail point of the spectra. It can be changed to other point, enter the
+corresponding energy value. The intention is to normalize at an energy value
+away from the peaks/features of interest.
+
+- `suv.lock_peak(data, refdata, x1=None, x2=None, E_col=0, I_col=9, I0_col=4)`:
+Locks peak position with respect to the reference data. It locks the maximum of
+intensity to the same energy; the range of peak search can be specified by input
+`x1` and `x2`. If no bounds are given, it will find the maximum in the whole
+data range.
+
+- `suv.calc_area(y, x, x_start=None, x_end=None)`:
+Calculates area under the curve for given `x` and `y` values. `x_start` and
+`x_end` can be specified to set the limit of integration region, if not provided
+whole range is integrated.
+
+See the notebook for some example usage.
+
+### Documentation development
+
+```console
+# install npm packages
+npm install
+
+# serve locally
+npm start
+
+# build
+npm run build
+
+# deploy to github
+npm run gh-deploy
+```
+
+### Python tests
+
+```console
+python3 -m unittest discover tests
+```
+

suvtools-1.0.0/README.md

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+<h1 align="center">SUV Tools</h1>
+
+<p align="center">
+  <a href="https://github.com/pranabdas/suvtools/actions/workflows/python-tests.yml"><img src="https://github.com/pranabdas/suvtools/actions/workflows/python-tests.yml/badge.svg" alt="Python tests status"></a>
+  <a href="https://github.com/pranabdas/suvtools/actions/workflows/deploy-gh-pages.yml"><img src="https://github.com/pranabdas/suvtools/actions/workflows/deploy-gh-pages.yml/badge.svg" alt="Deploy gh-pages status"></a>
+  <a href="https://github.com/pranabdas/suvtools/blob/master/LICENSE"><img src="https://img.shields.io/github/license/sourcerer-io/hall-of-fame.svg?colorB=A31F34"></a>
+  <a href="https://github.com/pranabdas/suvtools/releases/latest"><img src="https://img.shields.io/github/v/release/pranabdas/suvtools.svg" alt="Latest Release"/></a>
+</p>
+
+
+Visit the project homepage <https://pranabdas.github.io/suvtools/>
+
+## Quick start
+
+Install latest stable release:
+```console
+pip3 install --upgrade suvtools
+```
+
+Import suvtools into your project:
+```python
+import suvtools as suv
+```
+
+**Modules:**
+
+- `suv.load("datafile.txt", scan=None)`: It will return a two dimensional array
+with columns for various parameters. If the second argument, i.e., the scan
+number is not specified, the code will read the last scan from the file.
+
+- `suv.fit_gauss(x, y, a=None, x0=None, sigma=None, xmin=None, xmax=None, num=1000)`:
+returns x, Gaussian fitted y values, and prints out relevant parameters. `xmin`
+and `xmax` determines the range to fit. If `xmin` and `xmax` are not provided,
+whole range is used. `num` determines the number of points returned in `x_fit`
+and `y_fit`.
+
+- `suv.fit_lorentz(x, y, a=None, x0=None, gamma=None, xmin=None, xmax=None, num=1000)`:
+returns x, Lorentzian fitted y values, and prints out relevant parameters.
+`xmin` and `xmax` determines the range to fit. If `xmin` and `xmax` are not
+provided, whole range is used. `num` determines the number of points returned in
+`x_fit` and `y_fit`.
+
+- `suv.save_csv("datafile.txt", csvname=None, scan=None)`: saves scan to a csv
+file. The file will be saved in the save directory as `datafile` with name
+`datafile.csv` unless  `csvname` is specified. Like the `load` module, if the
+scan number is not specified, it will read the last scan from the file.
+
+- `suv.norm_bg(energy, intensity, x1, x2, x_norm_loc=None)`:
+Removes linear background, and normalizes the data. x1, x2 are energy values
+that determines the slope of the background. By default the normalization done
+at the tail point of the spectra. It can be changed to other point, enter the
+corresponding energy value. The intention is to normalize at an energy value
+away from the peaks/features of interest.
+
+- `suv.lock_peak(data, refdata, x1=None, x2=None, E_col=0, I_col=9, I0_col=4)`:
+Locks peak position with respect to the reference data. It locks the maximum of
+intensity to the same energy; the range of peak search can be specified by input
+`x1` and `x2`. If no bounds are given, it will find the maximum in the whole
+data range.
+
+- `suv.calc_area(y, x, x_start=None, x_end=None)`:
+Calculates area under the curve for given `x` and `y` values. `x_start` and
+`x_end` can be specified to set the limit of integration region, if not provided
+whole range is integrated.
+
+See the notebook for some example usage.
+
+### Documentation development
+
+```console
+# install npm packages
+npm install
+
+# serve locally
+npm start
+
+# build
+npm run build
+
+# deploy to github
+npm run gh-deploy
+```
+
+### Python tests
+
+```console
+python3 -m unittest discover tests
+```

suvtools-1.0.0/pyproject.toml

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+[tool.poetry]
+name = "suvtools"
+version = "1.0.0"
+description = "Python library for analyzing and visualizing SSLS SUV Beamline data."
+authors = ["Pranab Das"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://pranabdas.github.io/suvtools/"
+repository = "https://github.com/pranabdas/suvtools"
+documentation = "https://pranabdas.github.io/suvtools/docs/"
+keywords = [
+    "python", "data-analysis", "matplotlib", "materials-science",
+    "surface-science", "condensed-matter-physics", "photoelectron-spectroscopy",
+    "arpes"]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+matplotlib = "^3.9.2"
+numpy = "^2.0.2"
+pandas = "^2.2.3"
+scipy = "^1.13.1"
+
+[tool.poetry.group.dev.dependencies]
+autopep8 = "^2.3.1"
+jupyterlab = "^4.2.5"
+
+[tool.poetry.group.tests.dependencies]
+psutil = "^6.0.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

suvtools-1.0.0/src/suvtools/__init__.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: SUV tools
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+"""
+from .load import load
+from .fit_gauss import fit_gauss
+from .fit_lorentz import fit_lorentz
+from .save_csv import save_csv
+from .norm_bg import norm_bg
+from .lock_peak import lock_peak
+from .calc_area import calc_area

suvtools-1.0.0/src/suvtools/calc_area.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Calculate area under the curve
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+area = suv.calc_area(y, x, x_end=None, x_end=None)
+"""
+
+
+def calc_area(y, x, x_start=None, x_end=None):
+    import numpy as np
+
+    if x_start:
+        start_index = np.argmin(abs(x - x_start))
+    else:
+        start_index = 0
+
+    if x_end:
+        end_index = np.argmin(abs(x - x_end))
+    else:
+        end_index = -1
+
+    return np.trapezoid(y[start_index:end_index], x[start_index:end_index])

suvtools-1.0.0/src/suvtools/fit_gauss.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Fit peaks with Gaussian distribution
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+data = suv.fit_gauss(x, y, a=None, x0=None, sigma=None, xmin=None, xmax=None)
+"""
+
+
+def fit_gauss(x, y, a=None, x0=None, sigma=None, xmin=None, xmax=None, num=1000):
+    import numpy as np
+    from scipy import optimize
+
+    def gauss(x, a, x0, sigma):
+        return a * np.exp(-((x - x0) ** 2) / (2 * sigma**2))
+
+    if xmin:
+        xmin = float(xmin)
+        xmin_id = np.argmin(abs(x - xmin))
+        x = x[xmin_id:]
+        y = y[xmin_id:]
+    else:
+        xmin = x[0]
+
+    if xmax:
+        xmax = float(xmax)
+        xmax_id = np.argmin(abs(x - xmax))
+        x = x[:xmax_id]
+        y = y[:xmax_id]
+    else:
+        xmax = x[-1]
+
+    if not a:
+        a = max(y)
+
+    if not x0:
+        x0 = x[np.argmax(y)]
+
+    if not sigma:
+        sigma = abs(x[-1] - x[0]) / 10
+
+    params, _ = optimize.curve_fit(gauss, x, y, p0=[a, x0, sigma])
+
+    print(
+        "\n#---- Gaussian fitting parameters ----#\na =",
+        params[0],
+        "\nx0 =",
+        params[1],
+        "\nsigma =",
+        params[2],
+        "\nFWHM =",
+        2.355 * params[2],
+        "\n#----------------------------------------#",
+    )
+
+    fit_x = np.linspace(xmin, xmax, num)
+    fit_y = gauss(fit_x, params[0], params[1], params[2])
+
+    return fit_x, fit_y

suvtools-1.0.0/src/suvtools/fit_lorentz.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Fit peaks with Lorentzian distribution
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+data = suv.fit_lorentz(x, y, a=None, x0=None, gamma=None, xmin=None, xmax=None)
+"""
+
+
+def fit_lorentz(x, y, a=None, x0=None, gamma=None, xmin=None, xmax=None, num=1000):
+    import numpy as np
+    from scipy import optimize
+
+    def lorentz(x, a, x0, gamma):
+        return a * gamma**2 / (np.pi * gamma * ((x - x0) ** 2 + gamma**2))
+
+    if xmin:
+        xmin = float(xmin)
+        xmin_id = np.argmin(abs(x - xmin))
+        x = x[xmin_id:]
+        y = y[xmin_id:]
+    else:
+        xmin = x[0]
+
+    if xmax:
+        xmax = float(xmax)
+        xmax_id = np.argmin(abs(x - xmax))
+        x = x[:xmax_id]
+        y = y[:xmax_id]
+    else:
+        xmax = x[-1]
+
+    if not a:
+        a = max(y)
+
+    if not x0:
+        x0 = x[np.argmax(y)]
+
+    if not gamma:
+        gamma = abs(x[-1] - x[0]) / 10
+
+    params, _ = optimize.curve_fit(lorentz, x, y, p0=[a, x0, gamma])
+
+    print(
+        "\n#---- Lorentzian fitting parameters ----#\na =",
+        params[0],
+        "\nx0 =",
+        params[1],
+        "\ngamma =",
+        params[2],
+        "\nFWHM =",
+        2 * params[2],
+        "\n#---------------------------------------#",
+    )
+
+    fit_x = np.linspace(xmin, xmax, num)
+    fit_y = lorentz(fit_x, params[0], params[1], params[2])
+
+    return fit_x, fit_y

suvtools-1.0.0/src/suvtools/load.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Load SUV data
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+data = suv.load("data.txt", 12)
+"""
+
+
+def load(filename, scan=None):
+    import numpy as np
+    import urllib.request
+    import itertools
+
+    if (filename[:7] == "http://") or (filename[:8] == "https://"):
+        web = True
+    else:
+        web = False
+
+    if web:
+        try:
+            headers = {"User-Agent": "Mozilla/5.0"}
+            req = urllib.request.Request(url=filename, headers=headers)
+            contents = urllib.request.urlopen(req).read().decode()
+            contents = contents.splitlines()
+        except:
+            print("Could not read url.")
+
+    else:
+        fid = open(filename, "r")
+        if fid.mode == "r":
+            contents = fid.read()
+        fid.close()
+        contents = contents.splitlines()
+
+    # remove empty lines
+    # contents = list(filter(None, contents))
+
+    # find scan id and corresponding line numbers
+    scan_id = []
+    line_id = []
+
+    for line in range(len(contents)):
+        line_content = contents[line].split(" ")
+        if line_content[0] == "#S":
+            scan_id.append(int(line_content[1]))
+            line_id.append(line)
+
+    scan_id = np.array(scan_id)
+    # Determine the lines to read for specific scan
+    # Default scan set to the last scan
+    if not scan:
+        scan = scan_id[-1]
+
+    # In case given scan does not exist in the file
+    if scan not in scan_id:
+        print("Error: scan not found!")
+        return
+    else:
+        line_start = line_id[np.where(scan_id == scan)[0][0]]
+
+        if scan == scan_id[-1]:
+            line_end = len(contents)
+        else:
+            line_end = line_id[np.where(scan_id == scan)[0][0] + 1] - 1
+
+    # Extract the column names
+    # for line in range(line_end-line_start):
+    #     line_content = contents[line+line_start].split(' ')
+    #     if line_content[0]=='#L':
+    #         colnames=line_content
+    #         colnames.pop(0)
+    #         colnames = list(filter(None, colnames))
+    #     break
+
+    # print("Scan #", scan, "loaded. Data columns are: \n", colnames)
+
+    lines_to_read = itertools.islice(open(filename), line_start, line_end)
+    filtered_lines = itertools.dropwhile(lambda x: x.strip()[0] == "#", lines_to_read)
+
+    return np.loadtxt(filtered_lines)

suvtools-1.0.0/src/suvtools/lock_peak.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Lock the peaks at same energy location
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+data = suv.lock_peak(data, refdata, x1=None, x2=None, E_col=0, I_col=9, I0_col=4)
+"""
+
+
+def lock_peak(data, refdata, x1=None, x2=None, E_col=0, I_col=9, I0_col=4):
+    import numpy as np
+
+    if data.shape != refdata.shape:
+        print("Error! Data and reference data must have same dimensions!")
+        return
+
+    if not x1:
+        x1 = refdata[0, E_col]
+    if not x2:
+        x2 = refdata[-1, E_col]
+
+    x1_id = np.argmin(abs(refdata[:, E_col] - x1))
+    x2_id = np.argmin(abs(refdata[:, E_col] - x2))
+
+    ref_peak_id = np.argmax(refdata[x1_id:x2_id, I_col] / refdata[x1_id:x2_id, I0_col])
+
+    peak_id = np.argmax(data[x1_id:x2_id, I_col] / data[x1_id:x2_id, I0_col])
+
+    diff_id = peak_id - ref_peak_id
+
+    if diff_id > 0:
+        for _ in range(diff_id):
+            data = np.delete(data, 0, 0)
+            data = np.vstack((data, data[-1, :]))
+    elif diff_id < 0:
+        for _ in range(abs(diff_id)):
+            data = np.delete(data, -1, 0)
+            data = np.vstack((data[0, :], data))
+
+    data[:, E_col] = refdata[:, E_col]
+
+    return data

suvtools-1.0.0/src/suvtools/norm_bg.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Subtracts linear background and normalizes the data
+Version: 20240619
+@author: Pranab Das (GitHub: @pranabdas)
+normalized_intensity = suv.norm_bg(energy, intensity, x1, x2, x_norm_loc=None)
+"""
+
+
+def norm_bg(energy, intensity, x1, x2, x_norm_loc=None):
+    import numpy as np
+
+    y1 = intensity[np.argmin(abs(energy - x1))]
+    y2 = intensity[np.argmin(abs(energy - x2))]
+
+    if x_norm_loc:
+        x_norm_loc = np.argmin(abs(energy - x_norm_loc))
+    else:
+        x_norm_loc = -1
+
+    m = (y2 - y1) / (x2 - x1)  # slope
+    c = y1 - (m * x1)  # intersection
+
+    bg = (m * energy) + c
+    intensity -= bg
+    return intensity / intensity[x_norm_loc]

suvtools-1.0.0/src/suvtools/save_csv.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Program: Export SUV data in CSV format
+Version: 20220214
+@author: Pranab Das (GitHub: @pranabdas)
+data = suv.save_csv(filename, csvname=None, scan=None)
+"""
+
+
+def save_csv(filename, csvname=None, scan=None):
+    import numpy as np
+    import pandas as pd
+    import os
+    import warnings
+
+    fid = open(filename, "r")
+    contents = fid.read()
+    fid.close()
+    contents = contents.splitlines()
+
+    # find scan id and corresponding line numbers
+    scan_id = []
+    line_id = []
+
+    for line in range(len(contents)):
+        line_content = contents[line].split(" ")
+        if line_content[0] == "#S":
+            scan_id.append(int(line_content[1]))
+            line_id.append(line)
+
+    # determine the lines to read for specific scan
+    # default scan set to the last scan
+    if not scan:
+        scan = scan_id[-1]
+
+    # if given scan does not exist in the file
+    if scan not in scan_id:
+        print("Error! Scan not found!")
+        return
+    else:
+        line_start = line_id[scan - 1]
+        if scan == scan_id[-1]:
+            line_end = len(contents)
+        else:
+            line_end = line_id[scan] - 1
+
+    if not csvname:
+        csvname = filename + "_scan_" + str(scan) + ".csv"
+
+    if os.path.isfile(csvname):
+        if csvname[-4:] == ".csv":
+            csvname = csvname[:-4]
+        csvname = csvname + "_copy.csv"
+
+    # Extract the column names
+    for line in range(line_end - line_start):
+        line_content = contents[line + line_start].split(" ")
+        if line_content[0] == "#L":
+            colnames = line_content
+            colnames.pop(0)
+            colnames = list(filter(None, colnames))
+
+    # suppress numpy warning related to max_rows behavior
+    with warnings.catch_warnings():
+        warnings.filterwarnings(action="ignore")
+        data = np.loadtxt(
+            filename,
+            comments="#",
+            skiprows=(line_start - 1),
+            max_rows=(line_end - line_start),
+        )
+
+    # convert to dataframe
+    data = pd.DataFrame(data, columns=colnames)
+    data.to_csv(csvname, index=False)
+    print("Saved data to file:", csvname)