Fixed Spelling Mistake

JBeckwith · JBeckwith · commit c6feccc258bc · 2024-04-25T11:24:56.000+01:00
diff --git a/Example_CVE_Analysis.ipynb b/Example_CVE_Analysis.ipynb
@@ -70,7 +70,7 @@
    "id": "c1896d48-4e54-4c3a-b288-d905364ea2bd",
    "metadata": {},
    "source": [
-    "Then, we analyse it using our maximum likelihood estimator function."
+    "Then, we analyse it using our CVE estimator function."
    ]
   },
   {
@@ -117,7 +117,7 @@
    "id": "0e10ab24-f180-4f27-95f9-d0002fc296d0",
    "metadata": {},
    "source": [
-    "This may be not exactly correct! We can quickly simulate 1,000 different actualisations of our coordinate to confirm that on average our MLE does well."
+    "This may be not exactly correct! We can quickly simulate 1,000 different actualisations of our coordinate to confirm that on average our CVE does well."
    ]
   },
   {
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,28 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'pyDiffusion_LeeLab'
+copyright = '2024, Joseph S. Beckwith'
+author = 'Joseph S. Beckwith'
+release = 'v0.1.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,20 @@
+.. pyDiffusion_LeeLab documentation master file, created by
+   sphinx-quickstart on Thu Apr 25 11:23:00 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to pyDiffusion_LeeLab's documentation!
+==============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/src/LangevinFunctions.py b/src/LangevinFunctions.py
@@ -86,14 +86,16 @@ def BrownianTrans_Ideal(self, DT, n_d, deltaT, N):
 
     def BrownianRot(self, DR, TStep, NSteps):
         """ BrownianRot function
-        # generates random rotational motion
-        # using DR and TStep
-        # ================INPUTS============= 
-        # DR is rotational diffusion coefficient
-        # TStep is time step relative to DT
-        # NSteps is number of steps to simulate
-        # ================OUTPUT============= 
-        # sph_coords are theta, phi over time """
+            generates random rotational motion
+            using DR and TStep
+        
+        Args:
+            DR (float): rotational diffusion coefficient
+            TStep (float): time step relative to DT
+            NSteps (int): number of steps to simulate
+        
+        Returns:
+            sph_coords (np.3Darray): are theta, phi over time """
 
         # generate spherical coordinates using method of Hunter, G. L.;
         # Edmond, K. V.; Elsesser, M. T.; Weeks, E. R. 
diff --git a/src/PlottingFunctions.py b/src/PlottingFunctions.py
@@ -31,11 +31,18 @@ def __init__(self, poster=False):
     def two_column_plot(self, nrows=1, ncolumns=1, heightratio=[1], widthratio=[1], height=0):
         """ two_column_plot function
         takes data and makes a two-column width figure
-        ================INPUTS============= 
-        npanels is panel matrix
-        ratios is size ratios of panels
-        ================OUTPUT============= 
-        fig, axs are figure objects """
+        
+        Args:
+            nrows (int): number of rows
+            ncolumns (int): number of columns
+            heightratio (np.1darray): array of same length as number of rows
+            widthratio (np.1darray): array of same length as number of columns
+            height (float): if set, figure will be this height
+        
+        Returns:
+            fig (figure object): figure
+            axs (axes object): axes
+            """
         
         # first, check everything matches
         try:
@@ -92,82 +99,20 @@ def two_column_plot(self, nrows=1, ncolumns=1, heightratio=[1], widthratio=[1],
                     axs[i,j].yaxis.set_tick_params(width=0.5, length=lw*4)
                     axs[i,j].tick_params(axis='both', pad=1.2)
         return fig, axs
-    
-    def one_column_multirow_plot(self, nrows=1, ncolumns=1, heightratio=[1], widthratio=[1], height=0):
-        """ one_column_multirow_plot function
-        takes data and makes a one-column width figure
-        ================INPUTS============= 
-        npanels is panel matrix
-        ratios is size ratios of panels
-        ================OUTPUT============= 
-        fig, axs are figure objects """
-        
-        # first, check everything matches
-        try:
-            if len(heightratio) != nrows:
-                raise Exception('Number of height ratios incorrect')
-            if len(widthratio) != ncolumns:
-                raise Exception('Number of width ratios incorrect')
-        except Exception as error:
-            print('Caught this error: ' + repr(error))
-            return
-        
-        if self.poster == True:
-            fontsz = 12
-            lw = 1
-        else:
-            fontsz = 7
-            lw = 1
-
-        xsize = 3.33 # 3.33 inches for one-column figure
-        if height is not None:
-            ysize = np.min([height, 8.25]) # maximum size in y can be 8.25
-        else:
-            ysize = np.min([3.5*nrows, 8.25]) # maximum size in y can be 8.25
-        
-        plt.rcParams['figure.figsize'] = [xsize, ysize]
-        plt.rcParams['font.size'] = fontsz
-        plt.rcParams['svg.fonttype'] = 'none'
-        matplotlib.rcParams['pdf.fonttype'] = 42
-        matplotlib.rcParams['ps.fonttype'] = 42
-        plt.rcParams['axes.linewidth'] = lw # set the value globally
-        
-        fig, axs = plt.subplots(nrows, ncolumns, height_ratios=heightratio, 
-                                width_ratios=widthratio) # create number of panels
-
-
-        # clean up axes, tick parameters
-        if nrows*ncolumns == 1:
-            axs.xaxis.set_tick_params(width=lw, length=lw*4)
-            axs.yaxis.set_tick_params(width=lw, length=lw*4)
-            axs.tick_params(axis='both', pad=1.2)
-        elif nrows*ncolumns == 2:
-            for i in np.arange(2):
-                 axs[i].xaxis.set_tick_params(width=lw, length=lw*4)
-                 axs[i].yaxis.set_tick_params(width=lw, length=lw*4)
-                 axs[i].tick_params(axis='both', pad=1.2)
-        elif nrows*ncolumns == len(widthratio):
-            for i in np.arange(len(widthratio)):
-                 axs[i].xaxis.set_tick_params(width=lw, length=lw*4)
-                 axs[i].yaxis.set_tick_params(width=lw, length=lw*4)
-                 axs[i].tick_params(axis='both', pad=1.2)            
-        else:
-            for i in np.arange(nrows):
-                for j in np.arange(ncolumns):
-                    axs[i,j].xaxis.set_tick_params(width=0.5, length=lw*4)
-                    axs[i,j].yaxis.set_tick_params(width=0.5, length=lw*4)
-                    axs[i,j].tick_params(axis='both', pad=1.2)
-        return fig, axs
 
     def one_column_plot(self, npanels=1, ratios=[1], height=None):
         """ one_column_plot function
         takes data and makes a one-column width figure
-        ================INPUTS============= 
-        npanels is number of panels in the figure
-        ratios is size ratios of panels
-        height is figure height
-        ================OUTPUT============= 
-        fig, axs are figure objects """
+        
+        Args:
+            npanels (int): number of panels in the figure
+            ratios (np.1darray): size ratios of panels
+            height (float): figure height
+        
+        Returns:
+            fig (figure object): figure
+            axs (axes object): axes
+            """
         
         # first, check everything matches
         try:
@@ -251,18 +196,20 @@ def histogram_plot(self, axs, data, bins, xlim=None, ylim=None,
         histcolor='gray', xaxislabel='x axis', alpha=1, histtype='bar', density=True): 
         """ histogram_plot function
         takes data and makes a histogram
-        ================INPUTS============= 
-        data is data
-        bins are bins
-        xlim is x limits; default is None (which computes max/min)
-        ylim is y limits; default is None (which lets it keep its default)
-        histcolor is histogram colour (default is gray)
-        xaxislabel is x axis label (default is 'x axis')
-        alpha is histogram transparency (default 1)
-        density is if to plot as pdf, default yes
-        histtype is histogram type, default bar
-        ================OUTPUT============= 
-        axs is axis object """
+        
+        Args:
+            data (np.1darray): data array
+            bins (np.1darray): bin array
+            xlim (boolean or list of two floats): default is None (which computes min/max of x), otherwise provide a min/max
+            ylim (boolean or list of two floats): default is None (which computes min/max of y), otherwise provide a min/max
+            histcolor (string): histogram colour (default is gray)
+            xaxislabel (string): x axis label (default is 'x axis')
+            alpha (float): histogram transparency (default 1)
+            histtype (string): histogram type, default bar
+            density (boolean): if to plot as pdf, default True
+        
+        Returns:
+            axs (axis): axis object """
         if self.poster == True:
             fontsz = 15
         else:
@@ -286,21 +233,20 @@ def histogram_plot(self, axs, data, bins, xlim=None, ylim=None,
     def scatter_plot(self, axs, x, y, xlim=None, ylim=None, label='',
         edgecolor='k', facecolor='white', s=5, lw=0.75, xaxislabel='x axis', yaxislabel='y axis', alpha=1):
         """ scatter_plot function
-        takes data and makes a scatter plot
-        ================INPUTS============= 
-        x is x data
-        y os y data
-        xlim is x limits; default is None (which computes max/min)
-        ylim is y limits; default is None (which computes max/min)
-        label is label; default is nothing
-        edgecolor is edge colour; default is black
-        facecolor is face colour; default is white
-        s is size of scatter point; default is 5
-        lw is line width (default 0.75)
-        xaxislabel is x axis label (default is 'x axis')
-        yaxislabel is y axis label (default is 'y axis')
-        ================OUTPUT============= 
-        axs is axis object """
+        takes scatter data and makes an scatter plot
+        
+        Args:
+            xdata (np.1darray): scatter points, x
+            ydata (np.1darray): scatter points, y
+            xlim (np.1darray): x limits
+            ylim (np.1darray): y limits
+            label (string): any annotation
+            edgecolor (string): colour of scatter plot edges
+            facecolor (string): colour of scatter point faces
+            alpha (float): transparency of points
+        
+        Returns:
+            axs (axis): axis object """
         if self.poster == True:
             fontsz = 15
         else:
@@ -322,19 +268,21 @@ def image_plot(self, axs, data, vmin=None, vmax=None, cmap='binary', cbar='on',
                    labelcolor='black', pixelsize=69, scalebarsize=5000, scalebarlabel=r'5$\,\mu$m', alpha=1):
         """ image_plot function
         takes image data and makes an image plot
-        ================INPUTS============= 
-        data is image
-        vmin is minimum pixel displayed (default 99.9%)
-        vmax is maximum pixel displayed (default 0.1%)
-        cmap is colour map used; default gray
-        cbarlabel is colour bar label; default intensity
-        label is any annotation
-        labelcolor is annotation colour
-        pixelsize is pixel size in nm for scalebar, default 69
-        scalebarsize is scalebarsize in nm, default 5000
-        scalebarlabel is scale bar label, default 5 um
-        ================OUTPUT============= 
-        axs is axis object """
+        
+        Args:
+            data (np.2darray): image
+            vmin (float): minimum pixel intensity displayed (default 0.1%)
+            vmax (float): minimum pixel intensity displayed (default 99.9%)
+            cmap (string): colour map used; default gray)
+            cbarlabel (string): colour bar label; default 'photons'
+            label (string): is any annotation
+            labelcolor (string): annotation colour
+            pixelsize (float): pixel size in nm for scalebar, default 110
+            scalebarsize (float): scalebarsize in nm, default 5000
+            scalebarlabel (string): scale bar label, default 5 um
+        
+        Returns:
+            axs (axis): axis object """
         if vmin is None:
             vmin = np.percentile(data.ravel(), 0.1)
         if vmax is None:

Original file line number	Diff line number	Diff line change
`@@ -70,7 +70,7 @@`
`70`	`70`	`"id": "c1896d48-4e54-4c3a-b288-d905364ea2bd",`
`71`	`71`	`"metadata": {},`
`72`	`72`	`"source": [`
`73`		`- "Then, we analyse it using our maximum likelihood estimator function."`
	`73`	`+ "Then, we analyse it using our CVE estimator function."`
`74`	`74`	`]`
`75`	`75`	`},`
`76`	`76`	`{`
`@@ -117,7 +117,7 @@`
`117`	`117`	`"id": "0e10ab24-f180-4f27-95f9-d0002fc296d0",`
`118`	`118`	`"metadata": {},`
`119`	`119`	`"source": [`
`120`		`- "This may be not exactly correct! We can quickly simulate 1,000 different actualisations of our coordinate to confirm that on average our MLE does well."`
	`120`	`+ "This may be not exactly correct! We can quickly simulate 1,000 different actualisations of our coordinate to confirm that on average our CVE does well."`
`121`	`121`	`]`
`122`	`122`	`},`
`123`	`123`	`{`