Working filters into the main body

Author: MichaelClerx

artefacts/README.md

@@ -14,17 +14,21 @@ The first notebook describes the uncompensated patch-clamp set up, and shows how
 
 In the second notebook we update the model to include the compensation circuitry commonly used in patch-clamp amplifiers.
 
-## Simulating a manual patch clamp experiment [![github](../img/github.svg)](artefacts-3-simulations.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-3-simulations.ipynb)
+## Modelling filters [![github](../img/github.svg)](artefacts-3-filtering.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-3-filtering.ipynb)
 
 (Unfinished) In this notebook, we walk through the steps of a manual patch-clamp experiment.
 
-## Simplified models [![github](../img/github.svg)](artefacts-4-simplified.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-4-simplified.ipynb)
+## Simulating a manual patch clamp experiment [![github](../img/github.svg)](artefacts-4-simulations.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-4-simulations.ipynb)
 
-In notebook number four we derive simplified models of the compensated voltage clamp setup, which can be used in fitting.
+(Unfinished) In this notebook, we walk through the steps of a manual patch-clamp experiment.
+
+## Simplified models [![github](../img/github.svg)](artefacts-5-simplified.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-5-simplified.ipynb)
+
+(Unfinished) In notebook number five we derive simplified models of the compensated voltage clamp setup, which can be used in fitting.
 
-## Summary [![github](../img/github.svg)](artefacts-5-summary.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-5-summary.ipynb)
+## Summary [![github](../img/github.svg)](artefacts-6-summary.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/fitting-notebooks/tree/artefacts/artefacts/artefacts-6-summary.ipynb)
 
-Finally, we present two simplified models (with currents in pA and currents in A/F), in equation & Myokit form.
+(Unfinished) Finally, we present two simplified models (with currents in pA and currents in A/F), in equation & Myokit form.
 
 ## Appendices
 

artefacts/appendix-A4-bessel-filters.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# Simulating a manual patch clamp experiment\n",
     "\n",
-    "In the [last notebook](./artefacts-2-compensation.ipynb) we completed our model of whole-cell patch clamp in voltage-clamp mode, with compensation circuitry.\n",
+    "In the [last notebook](./artefacts-3-filters.ipynb) we completed our model of whole-cell patch clamp in voltage-clamp mode.\n",
     "Here, we use this model to simulate a manual patch clamp experiment."
    ]
   },
@@ -1076,7 +1076,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

artefacts/appendix-A5-bessel-filter-odes.ipynb

@@ -264,6 +264,9 @@ def bode(magnitude, argument, axes=None, lo=1e-2, hi=1e5, **kwargs):
         ax1.set_xscale('log')
         ax1.set_xlabel('Angular frequency')
         ax1.set_ylabel('Phase shift (degrees)')
+        ax1.set_ylim(-195, 195)
+        ax1.set_yticks([-180, -90, 0, 90, 180])
+
         ax1.grid()
     else:
         ax0, ax1 = axes