More TODOs, confidence scale_down now stricter (uses minimum)!

environment.yml

@@ -16,13 +16,13 @@ dependencies:
   # Basic:
   - python=3.5  # TODO: upgrade to 3.6!
   - numpy=1.11
-  - scipy=0.19  # TODO: upgrade to 1.0 (if channels exist...)!
+  - scipy=1.0  # TODO: upgrade to 1.0 (if channels exist...)!
   - tqdm=4.14
   - scikit-image=0.13
   # Fast computation:
   - pyFFTW=0.10
   # File IO:
-  - hyperspy=1.3
+  - hyperspy=1.3  # TODO: Update as soon as 1.4 is out!
   - hyperspy-gui-ipywidgets=1.0
   # - hyperspy-gui-traitsui=1.0  # TODO: Optional! Delete when mayavi is gone!
   - h5py=2.7

pyramid/fielddata.py

@@ -554,7 +554,7 @@ class VectorData(FieldData):
         self.field = np.pad(self.field, ((0, 0), (pv[0], pv[1]), (pv[2], pv[3]), (pv[4], pv[5])),
                             mode='constant')
 
-    def crop(self, crop_values):
+    def crop(self, crop_values):  # TODO: bad copy&paste from pad?
         """Crop the current field distribution with zeros for each individual axis.
 
         Parameters
@@ -796,6 +796,14 @@ class VectorData(FieldData):
 
     # TODO: we have 2D and 3D plots, what about 1D line of vector arrows? Would be nice!
     # TODO: Make all a bit more flexible with squeeze (so dimensions are not as strict).
+    # TODO: Implement clip value for amplitude!
+    # TODO: ar_dens should work differently! do not show every n-th arrow! instead average:
+    # mag_overlay_vort = mag_data_vort.copy()
+    # mag_overlay_vort.scale_down(2)
+    # mag_overlay_vort.plot_quiver(axis=newax, coloring='uniform', bgcolor='white', show_mask=False,
+    #                              scalebar=False, hideaxes=True)
+    # # plt.savefig(directory + '/ch5-0-magnetic_distributions_v.png', bbox_inches='tight')
+    # plt.savefig(directory + '/ch5-0-magnetic_distributions_v.pdf', bbox_inches='tight')
 
     def plot_quiver(self, ar_dens=1, log=False, scaled=True, scale=1., b_0=None, qkey_unit='T',
                     coloring='angle', cmap=None,  # Used here and plot_streamlines!

pyramid/forwardmodel.py

@@ -33,7 +33,11 @@ __all__ = ['ForwardModel', 'ForwardModelCharge', 'DistributedForwardModel']
 # TODO: Hook points belong to the forward models (or better the CombinedForwardModel)
 # TODO: Maybe have one ForwardModel per image? (maybe not a good idea...?)
 # TODO: Build factory convenience functions for constructing CombinedForwardModels!
+# TODO: OR implement arithmetic + (combine) and * (concatenate one after the other)?!
 # TODO: DistributedForwardModel and CombinedForwardModel could be the same thing?!
+# TODO: Build vector class which should now what it contains (stack of PhaseMaps, VectorData,
+# TODO: ScalarData, Ramp parameters, or a combination) and according hook points!
+# TODO: Vector should be easily convertible to container classes (e.g. stack of PhaseMaps)!
 
 class ForwardModel(object):
     """Class for mapping 3D magnetic distributions to 2D phase maps.

pyramid/phasemap.py

@@ -295,7 +295,7 @@ class PhaseMap(object):
             mask = self.mask.reshape(dim_uv[0] // 2, 2, dim_uv[1] // 2, 2)
             self.mask = mask[:, 0, :, 0] & mask[:, 1, :, 0] & mask[:, 0, :, 1] & mask[:, 1, :, 1]
             self.confidence = self.confidence.reshape(dim_uv[0] // 2, 2,
-                                                      dim_uv[1] // 2, 2).mean(axis=(3, 1))
+                                                      dim_uv[1] // 2, 2).min(axis=(3, 1))
 
     def scale_up(self, n=1, order=0):
         """Scale up the phase map using spline interpolation of the requested order.

pyramid/plottools.py

@@ -28,6 +28,8 @@ FIGSIZE_DEFAULT = (6.7, 5)  # TODO: Apparently does not fit as well as before...
 FONTSIZE_DEFAULT = 20
 STROKE_DEFAULT = None
 
+# TODO: Cool: Plotting with four parameters for what to put in all four corners (with defaults)!
+
 # TODO: Replace by matplotlib styles!
 def pretty_plots(figsize=None, fontsize=None, stroke=None):
     """Set IPython formats (for interactive and PDF output) and set pretty matplotlib font."""
@@ -360,3 +362,31 @@ def format_axis(axis, format_axis=True, title='', fontsize=None, stroke=None, sc
             plt.tight_layout()
     # Return plotting axis:
     return axis
+
+# TODO: Implement stuff from Florian:
+def figsize(scale, height=None, textwidth=448.1309):
+    """
+    Calculates ideal matplotlib Figure size, according to the desirde scale.
+    :param scale: Fraction of Latex graphic input (scale*\textwidth)
+    :param height: figure height = figure width * height
+    :param textwidth:
+    :return:
+    """
+    fig_width_pt = textwidth                         # Get this from LaTeX using \the\textwidth
+    inches_per_pt = 1.0 / 72.27                       # Convert pt to inch
+    golden_mean = (np.sqrt(5.0) - 1.0) / 2.0            # Aesthetic ratio (you could change this)
+    fig_width = fig_width_pt * inches_per_pt * scale    # width in inches
+    if height is None:
+        fig_height = fig_width * golden_mean              # height in inches
+    else:
+        fig_height = fig_width * height
+    fig_size = [fig_width, fig_height]
+
+    return fig_size
+
+# TODO: Florians way of shifting axes labels (should already be in somewhere):
+# for i in [1, 3]:
+#     axs[i].yaxis.set_label_position('right')
+#     axs[i].tick_params(axis='both', labelleft='off', labelright='on', labelsize=5)
+#     axs[i].yaxis.tick_right()
+#     axs[i].get_yaxis().set_label_coords(1.22, 0.5)