Merge branch 'master' of github.com:vale981/fpraktikum

GL/scripts/out/figlist.txt

@@ -22,4 +22,40 @@
   \caption{}
   \label{fig:vortrag-stabdiag}
 \end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/kaustik/peakfit.pgf}
+  \caption{}
+  \label{fig:kaustik-peakfit}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/kaustik/peakfit.pgf}
+  \caption{}
+  \label{fig:kaustik-peakfit}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/kaustik/peakfit.pgf}
+  \caption{}
+  \label{fig:kaustik-peakfit}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/kaustik/peakfit.pgf}
+  \caption{}
+  \label{fig:kaustik-peakfit}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/kaustik/peakfit.pgf}
+  \caption{}
+  \label{fig:kaustik-peakfit}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/kaustik/kaust_red.pgf}
+  \caption{}
+  \label{fig:kaustik-kaust_red}
+\end{figure}
     

GL/scripts/util.py

@@ -3,6 +3,14 @@ import matplotlib
 import numpy as np
 import matplotlib.ticker as ticker
 import os
+from SecondaryValue import SecondaryValue
+from scipy.optimize import curve_fit
+from mpl_toolkits.mplot3d import Axes3D
+from matplotlib import cm
+import scipy.ndimage as ndimage
+from scipy.ndimage.measurements import label
+from scipy.ndimage.filters import maximum_filter
+from scipy.ndimage.morphology import generate_binary_structure, binary_erosion
 matplotlib.rcParams.update({
     'font.family': 'serif',
     'text.usetex': False,
@@ -49,3 +57,95 @@ def save_fig(fig, title, folder='unsorted', size=(5, 4)):
   \label{fig:''' + folder + '-' + title + '''}
 \end{figure}
     ''')
+
+
+def coordinates_to_position(x, y=None, reco_raster=3.375, absolute=False):
+    pos = x*reco_raster
+    if not absolute:
+        pos += reco_raster/2
+
+    return (pos, coordinates_to_position(y, reco_raster=reco_raster,
+                                   absolute=absolute)) \
+        if y is not None else pos
+
+def coordinates_error_to_position_error(x, y=None, reco_raster=3.375):
+    err = x*reco_raster
+    return (err, coordinates_error_to_position_error(y, reco_raster=reco_raster)) \
+        if y is not None else err
+
+def plot_reconstruction(reconstruction, fig=None, subplot=111, title=None,
+                      azim=-45, elev=50, save=None, **pyplot_args):
+    fig = fig if fig else plt.figure()
+    ax = fig.add_subplot(subplot, projection='3d')
+
+    ax.view_init(azim=azim, elev=elev)
+    ax.set_xlabel('x')
+    ax.set_ylabel('y')
+
+    if title:
+        ax.set_title(title)
+
+    x, y = np.arange(0, reconstruction.shape[0]),np.arange(0, reconstruction.shape[1])
+    x, y = np.meshgrid(x, y)
+
+    ax.plot_surface(x, y, reconstruction, cmap=cm.plasma,
+                    shade=True, **pyplot_args)
+    fig.tight_layout()
+
+    if save:
+        save_fig(fig, *save)
+    return fig, ax
+
+def gauss2d(xy, A, mx, my, sigma):
+    x, y = xy
+    return np.ravel(A*np.exp(-((x-mx)**2 + (y-my)**2)/(2*sigma**2)))
+
+def normalize(array):
+    tmp = array.copy()
+    tmp = tmp - tmp.min()
+    return tmp/tmp.max()
+
+
+def find_peak_positions(reconstruction, threshold=.1, save=None):
+    rec = reconstruction.copy()
+
+    # normalize
+    rec_normalized = normalize(rec)
+
+    # create grid with real coordinates
+    x, y = np.arange(0, rec.shape[0]), np.arange(0, rec.shape[1])
+    x, y = np.meshgrid(x, y)
+
+    # foodprint
+    neighborhood = generate_binary_structure(2,4)
+    local_max = maximum_filter(rec_normalized, footprint=neighborhood) > threshold
+
+    # extract peaks
+    features, num_labels = label(local_max)
+    sliced = ndimage.find_objects(features)
+
+    peaks = []
+
+    plotdim = 200 + num_labels*10
+    fig = plt.figure()
+
+    for i in range(1, num_labels + 1):
+        slc = sliced[i-1]
+
+        # mask input to only show one peak
+        masked = rec*(features == i)
+        # guess the peak position
+        guess = [1, (slc[1].start + slc[1].stop)/2, (slc[0].start + slc[0].stop)/2, 1]
+
+        # fit gauss
+        opt, cov = curve_fit(gauss2d, (x, y), np.ravel(masked), p0=guess)
+        cov = np.sqrt(np.diag(cov))
+        plot_reconstruction(gauss2d((x, y), *opt).reshape(*rec.shape),
+                            fig=fig, subplot=plotdim + i, elev=30, title=f"Fit Peak {i}")
+        plot_reconstruction(masked, fig=fig, subplot=plotdim + num_labels + i, elev=30, title=f"Peak {i}")
+
+        peaks += [cov]
+
+    if save:
+        save_fig(fig, save[0], save[1], size=(2,4))
+    return peaks

Lab_Report_LaTeX

@@ -1 +1 @@
-Subproject commit 6f7da8668c507f74760217c2e4c5f944f0d10b0d
+Subproject commit bc42f5fa1d5bdeddbe983f0fd653a5e0843c0f8f

PET/auswertung/out/figlist.txt

@@ -1810,4 +1810,232 @@
   \caption{}
   \label{fig:tom2-3dplot}
 \end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/source.pgf}
+  \caption{}
+  \label{fig:theory-source}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/projection.pgf}
+  \caption{}
+  \label{fig:theory-projection}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/source.pgf}
+  \caption{}
+  \label{fig:theory-source}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/projection.pgf}
+  \caption{}
+  \label{fig:theory-projection}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/source.pgf}
+  \caption{}
+  \label{fig:theory-source}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/projection.pgf}
+  \caption{}
+  \label{fig:theory-projection}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/source.pgf}
+  \caption{}
+  \label{fig:theory-source}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/projection.pgf}
+  \caption{}
+  \label{fig:theory-projection}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/source.pgf}
+  \caption{}
+  \label{fig:theory-source}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/projection.pgf}
+  \caption{}
+  \label{fig:theory-projection}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/source.pgf}
+  \caption{}
+  \label{fig:theory-source}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/projection.pgf}
+  \caption{}
+  \label{fig:theory-projection}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/convoluted.pgf}
+  \caption{}
+  \label{fig:theory-convoluted}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_simple.pgf}
+  \caption{}
+  \label{fig:theory-rec_simple}
+\end{figure}
+    
+\begin{figure}[H]\centering
+  \input{../auswertung/figs/theory/rec_filtered.pgf}
+  \caption{}
+  \label{fig:theory-rec_filtered}
+\end{figure}