Refactor modules (#1)

* refactor

parsers all in one spot

* Create pyproject.toml

* revise package imports

* Update andor.py

* lib dir was hiding

initially called lib, but was ignored due to gitignore.  renamed to `core` to avoid confusion with packaging

parsers.__init__ underwent some revision

* Create .pre-commit-config.yaml

* some cleanup

* Create pl_T_R_A.py

* Delete main2.py

* Create environment.yml

* fixes from flake8

simply example script issues

* example fixes

* flake8: fix bad references

* give a test

* Create __init__.py

* rename to troubleshoot pytest

* Update python-app.yml

* Update andor.py

* Update horiba.py

* Delete __init__.py

Author: ddkohler

.github/workflows/python-app.yml

@@ -28,6 +28,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/python-package-conda.yml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.10.0 # Replace by any tag/version: https://github.com/psf/black/tags
+    hooks:
+      - id: black
+        language_version: python3 # Should be a command that runs python3.6+
+        args: ["--line-length", "99"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: no-commit-to-branch
+        args: [-b master]
+
+default_language_version:
+  python: python3

.pre-commit-config.yaml

@@ -2,32 +2,32 @@
 Jin Group Tools for handling a variety of common data.
 Builds upon the WrightTools Data object.
 
-
-## Installation
-
-Basic:
-
-`pip install git+https://github.com/wright-group/makeitwright.git`
-
-iontof support is considered optional; if you need to use iontof data, use
-
-`pip install git+https://github.com/wright-group/makeitwright.git[iontof]`
-
-
 ## Features
 
 - a module for each instrument featured
-  - AFM
+  - AFM (Gwiddion)
   - Andor Neo Camera (Solis)
   - Becker and Hickl SPCM
   - Horiba LabRAM
   - Generic Images
   - ion TOF 
   - XRD (Bruker)
-- various data importers to create the WrightTools Data objects.
 - preset styles and routines for making quick figures
 
 
+## Installation
+
+### Basic
+
+`pip install git+https://github.com/wright-group/makeitwright.git`
+
+### IonTOF
+
+support for iontof data is optional; if you need to use iontof data, specify additional imports using:
+
+`pip install git+https://github.com/wright-group/makeitwright.git[iontof]`
+
+
 ## Examples
 
 TODO

README.md

@@ -1,16 +1,19 @@
 
-# Process Reflectance/Transmittance/Absorbance Data from Wright group
+# Process Reflectance/Transmittance/Absorbance Data from Wright group Microscope
 
 import pathlib
-import makeitwright.process.andor as andor
-from makeitwright.process.helpers import roi
-from makeitwright.parsers import parse
-from makeitwright.artists import setparams, setdpi
-from makeitwright.spectra import plot_spectra as plot
+import makeitwright as mw
+import matplotlib as mpl
 
 
-setparams()
-setdpi(150)
+andor = mw.andor
+roi = mw.helpers.roi
+parse = mw.parsers.parse
+plot = mw.spectra.plot_spectra
+
+
+mpl.rc(dpi=150)
+
 
 filepath = pathlib.Path().expanduser().resolve() / "Desktop/Research Data/Wright Table/Original/test"
 filename_R = "PEAPbBr4 R"

scripts/AbsProcessing.py renamed to examples/AbsProcessing.py

@@ -2,15 +2,14 @@
 # Process PL Data from Wright group
 
 import pathlib
-import makeitwright.process.andor as andor
-from makeitwright.process.helpers import roi
-from makeitwright.parsers import parse
-from makeitwright.artists import setparams, setdpi
-from makeitwright.spectra import plot_spectra as plot
+import makeitwright as mw
 
 
-setparams()
-setdpi(150)
+andor = mw.andor
+roi = mw.helpers.roi
+parse = mw.parsers.parse
+plot = mw.spectra.plot_spectra
+
 
 filepath = pathlib.Path().expanduser() / "Desktop" / "Research Data" / "Wright Table" / "Original" / "test"
 filename = "PEAPbI on FPEASnI PL 77K 4 2 hour wait for cool"

scripts/PLProcessing.py renamed to examples/PLProcessing.py

@@ -1,11 +1,12 @@
 import matplotlib as mpl
 from pathlib import Path
 
-from makeitwright.process import andor
+import makeitwright as mw
 
-from makeitwright.process.helpers import show, roi, set_label
-from makeitwright.parsers import parse
-from makeitwright.artists import plot
+andor = mw.andor
+roi = mw.helpers.roi
+parse = mw.parsers.parse
+plot = mw.artists.plot
 
 
 user_path = Path().expanduser().resolve()

scripts/main.py renamed to examples/main.py

@@ -1,58 +1,49 @@
 import pathlib
-import numpy as np
-import matplotlib.cm as cms
-import cmocean.cm as cmo
-from scipy.signal import savgol_filter as savgol
-from scipy.signal import medfilt2d
-from scipy.optimize import curve_fit
-from scipy.stats import pearsonr, spearmanr, ttest_ind
-import WrightTools as wt
+import matplotlib as mpl
+import makeitwright as mw
 
-import makeitwright.process.andor as andor
-import makeitwright.process.beckerhickl as becker
-import makeitwright.process.spectralprofile
 
-from makeitwright.process.helpers import show, roi, norm, set_label
-from makeitwright.parsers import parse
-from makeitwright.artists import setparams, setdpi
-from makeitwright.spectra import plot_spectra as plot
+roi = mw.helpers.roi
+parse = mw.parsers.parse
+andor = mw.andor
+becker = mw.beckerhickl
+plot = mw.spectra.plot_spectra
 
-setparams()
-setdpi(150)
+fp = pathlib.Path().expanduser().resolve() / r"Desktop/Research Data/Wright Table/Original"
 
-fp = pathlib.Path().expanduser().resolve() / r"Desktop/Research Data/Wright Table/Original"  # filepath name to folder
+# set plotting parameters
+mpl.rcParams['font.sans-serif'] = "Arial"
+mpl.rcParams['font.family'] = "sans-serif"
+mpl.rcParams['font.size'] = 14
+mpl.rcParams['figure.dpi'] = 300
+mpl.rcParams['lines.linewidth'] = 4
+mpl.rcParams['pcolor.shading'] = 'auto'
+mpl.rcParams['figure.dpi'] = 150
 
-
-#
 if True: # Plot PL
     data = parse(fp, keywords='4 hr.asc')
-    #andor.correct_PL_background(data, ybkg=[0, 20])
-    #y_profile = roi(data, {'wl': ([400, 800], 'sum')})                           # If need to check object area
-    #plot(y_profile)
     PL_ROI = roi(data, {'y': ([1021, 1047], 'average')})
     plot(PL_ROI, channel=0, xrange=[500, 850])
-    PL_output = open('C:/Users/kmfor/Desktop/Research Data/Wright Table/Original/4hr.txt', 'w')
+    PL_output = open(fp / '4hr.txt', 'w')
     PL_dataTrace = zip(PL_ROI.axes[0], PL_ROI.channels[0])
     for x in PL_dataTrace:
         PL_output.write(str(x[0])+'\t')
         PL_output.write(str(x[1])+'\n')
     PL_output.close()
 
-#
 if True: # Plot T/R/A
-    data = parse('C:/Users/kmfor/Desktop/Research Data/Wright Table/Original/For Chris/23_11_21/4ClPEASnI n1', keywords='Object 3')
+    data = parse(fp / 'For Chris/23_11_21/4ClPEASnI n1', keywords='Object 3')
     R = data[2]
     R_back = data[1]
     T = data[4]
     T_back = data[3]
-
 
     andor.compute_reflectance(R, R_back, dark_wavelength_range=None)
     y_profile = roi(R, {'wl': ([580, 750], 'sum')})                           # If need to check object area
     plot(y_profile)
     plot(R, channel=1, ROI={'y': ([1020, 1070], 'average')}, xrange=[580, 750]) #Currently at 10 x mag
     R_ROI = roi(R, {'y': ([1020, 1070], 'average')})
-    R_output = open('C:/Users/kmfor/Desktop/Research Data/Wright Table/Original/For Chris/23_11_21/4ClPEASnI n1/Object 3 R processed.txt', 'w')
+    R_output = open(fp / 'For Chris/23_11_21/4ClPEASnI n1/Object 3 R processed.txt', 'w')
     R_dataTrace = zip(R_ROI.axes[0], R_ROI.channels[1])
     for x in R_dataTrace:
         R_output.write(str(x[0])+'\t')
@@ -64,15 +55,15 @@
     # plot(y_profile)
     plot(T, channel=1, ROI={'y': ([1020, 1070], 'average')}, xrange=[580, 750])     # Current 10x mag, 100x mag 54-70
     T_ROI = roi(T, {'y': ([1020, 1070], 'average')})
-    T_output = open('C:/Users/kmfor/Desktop/Research Data/Wright Table/Original/For Chris/23_11_21/4ClPEASnI n1/Object 3 T Processed.txt', 'w')
+    T_output = open(fp / 'For Chris/23_11_21/4ClPEASnI n1/Object 3 T Processed.txt', 'w')
     T_dataTrace = zip(T_ROI.axes[0], T_ROI.channels[1])
     for x in T_dataTrace:
         T_output.write(str(x[0])+'\t')
         T_output.write(str(x[1])+'\n')
     T_output.close()
     #
     andor.compute_absorbance(R, T)
-    A_output = open('C:/Users/kmfor/Desktop/Research Data/Wright Table/Original/For Chris/23_11_21/4ClPEASnI n1/Object 3 A processed.txt', 'w')
+    A_output = open(fp / 'For Chris/23_11_21/4ClPEASnI n1/Object 3 A processed.txt', 'w')
     A_ROI = roi(T, {'y': ([1020, 1070], 'average')})                        # A is channel 2 in both R and T data objects
     plot(R, channel=2, ROI={'y': ([1020, 1070], 'average')}, xrange=[580, 750]) #Current 10x mag. can add vrange
     A_dataTrace = zip(A_ROI.axes[0], A_ROI.channels[2])

scripts/main2.py renamed to examples/pl_T_R_A.py

@@ -8,6 +8,15 @@
 from scipy.signal import savgol_filter
 from matplotlib import pyplot as plt
 
+import makeitwright as mw
+
+
+parse = mw.parsers.parse
+__at = mw.helpers.find_nearest()
+roi = mw.helpers.roi
+set_label = mw.helpers.set_label
+norm = mw.helpers.norm
+
 
 def lorentz_fit_2(data, channel='darksub', xrange='all', bounds=None, plot=False):
 
@@ -136,6 +145,7 @@ def test2(x, a1, u1, s1, a2, u2, s2):
 def residual(a, fit):
     return (a-fit)/a*100
 
+
 base = pathlib.Path().expanduser().resolve() / r'OneDrive/Documents/UW/research/data local/WG-microscope/biexciton-fluence-dependent-PL_20220909'
 fn1 = base / "n1BA"
 fn2 = base / 'n2BAMA_CRRsample'
@@ -201,7 +211,7 @@ def residual(a, fit):
     wlbkgsub = (d['sig'][:]-wlbkg)/exposure
     d.create_channel('constantbkgsub',values=constantbkgsub)
     d.create_channel('wlbkgsub',values=wlbkgsub)
-    set_label(d, 'wlbkgsub', "PL intensity (cps)")
+    # set_label(d, 'wlbkgsub', "PL intensity (cps)")
 
 bn1 = roi(n1raw,{'y':'sum'})
 bn2 = roi(n2raw,{'y':'sum'})

scripts/workup.py renamed to examples/workup.py

@@ -0,0 +1 @@
+0.0.1