fix links to images

docs/ifigures_api.md

@@ -4,7 +4,7 @@
 ::: ifigures.InteractiveFigure  
 
 !!! tip "Why use interactive figure?"
-    This is discussed in [Physics World blogpost and comment](../example_gallery/#motivation-and-goals). In short, we want to allow exploration of many untold stories and edge cases. To build intuition, connections and maybe get
+    This is discussed in [Physics World blogpost and comment](example_gallery.md/#motivation-and-goals). In short, we want to allow exploration of many untold stories and edge cases. To build intuition, connections and maybe get
     inspired for further work!
 
 !!! Example "Simple interactive figure"
@@ -89,7 +89,7 @@
     print(figure_example1.overallCaption)
 
     ```
-    ![static figure example](./assets/example_static.png)
+    ![static figure example](assets/example_static.png)
 
 
     `(a) Amplitude = 0.50, omega = 1.00, color = red, f(t) = amplitude * sin(omega*x). Highlighted time = 1.50, (b) Amplitude = 0.50, omega = 3.00, color = blue, f(t) = amplitude * sin(omega*x). Highlighted time = 1.60, (c) Amplitude = 0.50, omega = 1.00, color = red, f(t) = amplitude * cos(omega*x). Highlighted time = 1.50, (d) Amplitude = 0.50, omega = 3.00, color = blue, f(t) = amplitude * cos(omega*x). Highlighted time = 1.60`
@@ -102,22 +102,22 @@ Inputs for interactive figures are range sliders (including specially coloured `
 ::: ifigures.RangeWidget
 
 !!! Example "Example: a static snapshot of input control widget"
-    ![Range widget](./assets/widget_range.png)
+    ![Range widget](assets/widget_range.png)
 
 ::: ifigures.RangeWidgetViridis
 
 !!! Example "Example: a static snapshot of input control widget"
-    ![Range widget viridis for time](./assets/widget_range_viridis.png)
+    ![Range widget viridis for time](assets/widget_range_viridis.png)
 
 ::: ifigures.RadioWidget
 
 !!! Example "Example: a static snapshot of input control widget"
-    ![Radio widget](./assets/widget_radio_button.png)
+    ![Radio widget](assets/widget_radio_button.png)
 
 ::: ifigures.DropDownWidget
 
 !!! Example "Example: a static snapshot of input control widget"
-    ![Drop down widget](./assets/widget_dropdown.png)
+    ![Drop down widget](assets/widget_dropdown.png)
 
 ## Interactive timeline
 
@@ -157,7 +157,7 @@ Inputs for interactive figures are range sliders (including specially coloured `
     ```
     produces 
 
-    ![Annotation example](./assets/annotation_example.png)
+    ![Annotation example](assets/annotation_example.png)
 
 !!! tip "Why should one use annotations?"
     Modern figures in reserach papers are often dense with information,
@@ -201,14 +201,14 @@ Some special commands are defined by default for use in equation environment
     ```
     results in
 
-    ![highlighted equations](./assets/equation_example.png)
+    ![highlighted equations](assets/equation_example.png)
 
 ## Quantum state visualisations
 
 ::: ifigures.getComplexColor
 
 !!! example "Mapping complex numbers to colors"
-    ![Complex color mapping](./assets/complex_color_mapping.png){width=300px  align=right}
+    ![Complex color mapping](assets/complex_color_mapping.png){width=300px  align=right}
     Mapping of complex number $A e^{i \phi}$ with amplitude $A$ and phase $\phi$
     to colours used by the library.
     Note that  complementary colours correspond
@@ -271,7 +271,7 @@ Some special commands are defined by default for use in equation environment
     bs.plot(axis=ax1)
 
     ```
-    ![Bloch sphere example](./assets/bs_example.png)
+    ![Bloch sphere example](assets/bs_example.png)
 
     Example above shows Bloch sphere, with annotated key points of the sphere,
     state trajectory in time shown as line with time encoded in viridis gradient,
@@ -295,7 +295,7 @@ Some special commands are defined by default for use in equation environment
 
     plt.show()
     ```
-    ![tst](./assets/dm_example.png)
+    ![tst](assets/dm_example.png)
 
 !!! tip "Why use coloured density matrixes"
     They are capable of quickly conveying numerical results, arguably providing
@@ -343,7 +343,7 @@ Some special commands are defined by default for use in equation environment
     plt.show()
     ```
 
-    ![example of state with dynamics indicated](./assets/example_state.png)
+    ![example of state with dynamics indicated](assets/example_state.png)
 
     - State blob with color and size correspond to phase and amplitude
     - small gray dot on the blobs indicates phasor tip, to allow also for colour blind readout

ifigures/amoplots.py

@@ -801,7 +801,7 @@ def plot (self, axis:plt.axis, rho, visualise="with dots"):
                 referenceDots["x"].append(col)
                 referenceDots["y"].append(row)
 
-        RGB=np.dstack((R, G, B))
+        RGB=np.dstack((R, G, B)).transpose()
         axis.imshow(RGB)
 
         if (visualise == "with dots"):

ifigures/interact.py

@@ -465,16 +465,16 @@ def saveStaticFigure(self, fileName:str, values: List[List]=None, figuresPerRow=
         Args:
             fileName (str): filename with extension (e.g. `example.png`).
             values (List[List], optional): List of Lists of arguments. For each
-              one static panel will be created. If not specified will use
-              all the values provided by the Input widgets.
+                one static panel will be created. If not specified will use
+                all the values provided by the Input widgets.
             figuresPerRow (int, optional): Number of panels per final figure row.
             labelPanels (bool, optional): Should we label panels with `(a), (b), ...`
             dpi (int, optional): resolution in dots per inch.
             labelSize (int, optional): Label size for individual panels
             labelOffset (tuple, optional): Offset position of label.
             labelGenerator (_type_, optional): _description_.
             compress (bool, optional): Should we use [pngquant](https://pngquant.org/) to compress final
-              figure.
+                figure.
         """
         self.compress = compress
         names = [name for name in self.widgets]

ifigures/style.py

@@ -8,6 +8,7 @@
 import matplotlib.colors as mcolors
 import numpy as np
 import colorsys
+from typing import List
 from PIL import Image
 
 mpl.rcParams['xtick.minor.visible'] = True
@@ -155,7 +156,7 @@ def getColor(amplitude, phase, maxAmplitude):
     return (c[0], c[1], c[2], 1.0)
 
 
-def getComplexColor(complexNo:complex, maxAmplitude:float):
+def getComplexColor(complexNo:complex, maxAmplitude:float)->List[float]:
     """
     Get color for a complex numbers
 
@@ -170,7 +171,7 @@ def getComplexColor(complexNo:complex, maxAmplitude:float):
             white color for zero amplitude.
 
     Returns:
-        color as [red, green, blue, alpha]
+        List[float]: color as [red, green, blue, alpha]
     """
     angle = np.angle(complexNo)
     if angle < 0:

ifigures/widgets.py

@@ -129,7 +129,7 @@ def __init__(self, values:List[type[str | float]], name=None,
             values (List[type[str | float]]): drop down option values
             name (_type_, optional): _description_. 
             labels (List[str], optional): labels for drop down options. By default
-            they are same as values.
+                they are same as values.
             default (_type_, optional): _description_. 
             divclass (_type_, optional): _description_. 
             delimiter (str, optional): _description_.