NSFopen 2.2.1__tar.gz → 2.2.3__tar.gz

nsfopen-2.2.3/NSFopen/_version.py

@@ -0,0 +1 @@
+__version__ = "2.2.3"

{NSFopen-2.2.1 → nsfopen-2.2.3}/NSFopen/example/Force_Spectroscopy/Force_Spectroscopy.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # coding: utf-8
 
-# ## This script demonstrates how to open a Nanosurf Force Spectroscopy map and analyze the data using the DMT contact mechanics model 
+# ## This script demonstrates how to open a Nanosurf Force Spectroscopy map and analyze the data using the DMT contact mechanics model
 
 # In[1]:
 
@@ -16,23 +16,27 @@ from scipy.optimize import curve_fit
 
 from glob import glob
 
-filename = 'spectroscopy.nid'
-filename_large = 'spectroscopy_large.nid'
+filename = "spectroscopy.nid"
+filename_large = "spectroscopy_large.nid"
 
 
 # In[2]:
 
 
-# If USE_LARGE_MAP is True, then it will use the larger force-curve map, downloading if not already locally available 
+# If USE_LARGE_MAP is True, then it will use the larger force-curve map, downloading if not already locally available
 USE_LARGE_MAP = False
 
 
 # In[3]:
 
 
-if USE_LARGE_MAP and filename_large not in glob('*nid'):
+if USE_LARGE_MAP and filename_large not in glob("*nid"):
     import urllib.request
-    urllib.request.urlretrieve("https://www.dropbox.com/s/knzuh588g0uvjfi/spectroscopy_large.nid?dl=1", filename_large)
+
+    urllib.request.urlretrieve(
+        "https://www.dropbox.com/s/knzuh588g0uvjfi/spectroscopy_large.nid?dl=1",
+        filename_large,
+    )
     filename = filename_large
 elif USE_LARGE_MAP:
     filename = filename_large
@@ -47,20 +51,28 @@ data = afm.data
 param = afm.param
 
 # probe
-k = param.Tip.Prop0['Value']  # spring constant
-sens = param.Tip.Sensitivity['Value']  # deflection sensitivity (if needed)
+k = param.Tip.Prop0["Value"]  # spring constant
+sens = param.Tip.Sensitivity["Value"]  # deflection sensitivity (if needed)
 
 radius = 10e-9  # tip radius
 nu = 0.35  # Poisson ratio (between 0.35 and 0.5)
 
-spec_backward = data['Spec']['Backward']  # for DMT model we will use backward modulation
-d = spec_backward['Deflection']  # force channel
+direction = "Backward"  # Forward or Backward modulation
+
+spec_backward = data["Spec"][
+    direction
+]  # for DMT model we will use backward modulation
+d = spec_backward["Deflection"]  # force channel
 
 z_signal = list(spec_backward.index)
-z_chans = ['Z-Axis Sensor', 'Z-AxisSensor', 'Z-Axis']  # depending on system, Z-Axis channel may be labeled differently
+z_chans = [
+    "Z-Axis Sensor",
+    "Z-AxisSensor",
+    "Z-Axis",
+]  # depending on system, Z-Axis channel may be labeled differently
 available_chan = [i for i in z_signal if i in z_chans][0]
 
-z = data['Spec']['Backward'][available_chan]  # Z-axis data
+z = data["Spec"][direction][available_chan]  # Z-axis data
 
 sz = int(param.Spec.maps[4])  # Map size
 
@@ -72,6 +84,7 @@ extent = param.Spec.maps[:4]  # X and Y physical dimensions of map
 
 ## Functions
 
+
 # corrects for any baseline tilt
 def baseline_correct(x, y, degree=1, start=0, end=0.5):
     i0 = int(np.floor(len(x) * start))
@@ -90,14 +103,15 @@ def baseline_correct(x, y, degree=1, start=0, end=0.5):
 def DMT(x, *param):
     elast, depth, wadh = param
 
-    scale = 4./3. * elast * np.sqrt(radius) / (1 - nu**2)
+    scale = 4.0 / 3.0 * elast * np.sqrt(radius) / (1 - nu**2)
     x = x - depth
-    y = scale * np.sign(x) * np.abs(x)**(3./2.) - wadh
+    y = scale * np.sign(x) * np.abs(x) ** (3.0 / 2.0) - wadh
     return y
 
 
 def DMTfit(*args, maxForce=np.Inf):
     import time
+
     t = time.time()
     # args are: [separation, load (force)]
     if not isinstance(args[0], list):
@@ -108,7 +122,7 @@ def DMTfit(*args, maxForce=np.Inf):
         # x = x - y / spring_constant  # separation
         lenY = int(np.floor(len(y) * 0.8))
         a = min(y[lenY:])  # adhesion
-    
+
         i0 = np.where(y == a)[0][0]  # contact point estimator index
         i1 = np.where(y > maxForce)[0]  # max force index
 
@@ -118,13 +132,15 @@ def DMTfit(*args, maxForce=np.Inf):
             i1 = i1[0]
 
         try:
-            coeff, var_matrix = curve_fit(DMT, x[i0:i1], y[i0:i1], p0=[1e9, x[i0], -a])
+            coeff, var_matrix = curve_fit(
+                DMT, x[i0:i1], y[i0:i1], p0=[1e9, x[i0], -a]
+            )
         except RuntimeError:
             E.append(np.nan)
         else:
             E.append(max(coeff[0], 0))
 
-    print('Elapsed Time: %3.2f sec\n' % (time.time() - t))
+    print("Elapsed Time: %3.2f sec\n" % (time.time() - t))
     return np.array(E), (coeff, i0, i1)
 
 
@@ -135,7 +151,7 @@ def DMTfit(*args, maxForce=np.Inf):
 dd = [baseline_correct(z_, d_, start=0.5, end=0.8) for z_, d_ in zip(z, d)]
 
 # separation
-zz = [zz - dd/k for dd, zz in zip(dd, z)]
+zz = [zz - dd / k for dd, zz in zip(dd, z)]
 
 # elastic modulus
 Eb, _ = DMTfit(zz, dd)
@@ -159,14 +175,16 @@ Adh = toMap(adh, sz)
 # In[7]:
 
 
-fig, ax = plt.subplots(2, 2, figsize=(10, 8), gridspec_kw={'height_ratios': [2, 1]}, dpi=300)
+fig, ax = plt.subplots(
+    2, 2, figsize=(10, 8), gridspec_kw={"height_ratios": [2, 1]}, dpi=300
+)
 fig.tight_layout(w_pad=8.0, h_pad=1.0)
 
 im = ax.copy()
 
 cmap = "afmhot"  # colormap
-xlbl = 'X [$\mu$m]'
-ylbl = 'Y [$\mu$m]'
+xlbl = "X [$\mu$m]"
+ylbl = "Y [$\mu$m]"
 zlbl = ["Young's Modulus [GPa]", "Adhesion [nN]"]
 
 im[0, 0] = ax[0, 0].imshow(Ebim)
@@ -182,8 +200,7 @@ for i in range(2):
     cb.set_label(zlbl[i])
 
     ax[0, i].set(xlabel=xlbl, ylabel=ylbl)
-    ax[1, i].set(xlabel=zlbl[i], ylabel='Counts')
+    ax[1, i].set(xlabel=zlbl[i], ylabel="Counts")
 
 
 plt.show()
-

{NSFopen-2.2.1 → nsfopen-2.2.3}/NSFopen/process/__init__.py

@@ -5,4 +5,4 @@ Created on Sat Oct 12 12:43:59 2019
 @author: Edward
 """
 
-from . process import process
+from . process import process, colormaps

nsfopen-2.2.3/NSFopen/process/colormaps.py

@@ -0,0 +1,71 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu May 23 13:04:53 2024
+
+@author: nelson
+"""
+
+import numpy as np
+import pandas as pd
+import os
+
+from matplotlib.colors import LinearSegmentedColormap
+
+
+class colors:
+    def __init__(self, name=None, gwy_dir=None, **kwargs):
+        self.name = name
+        self.gwy_dir = gwy_dir
+        if not gwy_dir:
+            self.gwy_dir = (
+                "C:\\Program Files\\Gwyddion\\share\\gwyddion\\gradients\\"
+            )
+        custom = ["BlueBlackRed"]
+        gwy_list = os.listdir(self.gwy_dir)
+
+        cmaps = {}
+        cmaps["Custom"] = custom
+        cmaps["Gwyddion"] = gwy_list
+
+        if name in gwy_list:
+            cmap = self.gwy_cmap()
+        elif name in custom:
+            cmap = self.custom()
+        else:
+            print("Name Not Found\n")
+            print("Use one of the following choices:\n")
+            print({x for v in cmaps.values() for x in v})
+            cmap = []
+        self.cmap = cmap
+        self.cmap_list = cmaps
+
+    def gwy_cmap(self):
+        cmap = pd.read_csv(
+            self.gwy_dir + self.name,
+            sep=" ",
+            header=None,
+            skiprows=1,
+            index_col=0,
+        )
+        nodes = cmap.index.values
+        colors = cmap.values
+
+        return LinearSegmentedColormap.from_list(
+            self.name, list(zip(nodes, colors))
+        )
+
+    def custom(self):
+        if self.name == "BlueBlackRed":
+            # Blue-Black-Red
+            start = np.array(
+                [0.6196078431372549, 0.792156862745098, 0.8823529411764706]
+            )
+            mid = np.array([0, 0, 0])
+            end = np.array(
+                [0.9882352941176471, 0.5725490196078431, 0.4470588235294118]
+            )
+            nodes = [0, 0.5, 1]
+
+        return LinearSegmentedColormap.from_list(
+            self.name, list(zip(nodes, [start, mid, end]))
+        )