Rl/add motility analysis notebook (#18)

* Create 2_Motility_Analysis_Pools.ipynb

* Update 1_Compute-Summary-Motility-Metrics.ipynb

add units to table and reformat a few cells.

* Update 2_Motility_Analysis_Pools.ipynb

subset of metrics for bivariate distributions

* fix legend

* fix legend

* Create 3_Scale-to-Pools.ipynb

* Create 4_PCA.ipynb

* update notebook formatting

* reduce subset of metrics

* rename notebooks

* update input directories for published dataset

* refactor: substrate --> vessel

* calculate angular change as a rolling average

* Create S1_Quality-Control.ipynb

* remove unused import

* Update S1_Quality-Control.ipynb

* change table style in docs

* Update 1_Compute-Summary-Motility-Metrics.ipynb

- add documentation
- move experimental parameters to ../data/experimental_parameters.json
- remove superfluous plot

* motility metrics for cc124 instead of cc1373

* Create experimental_parameters.json

* Create 2_Quality-Control.ipynb

* Delete 2_Analyze-Motility-in-Pools.ipynb

* Delete 3_Compare-Pools-vs-Wells.ipynb

* Delete 4_Perform-PCA.ipynb

* Delete S1_Quality-Control.ipynb

* linting: remove unused imports

* Rename notebooks

- rename notebook 2 based off Keith's suggestion from code review on #18
- surprising (to me at least) that switching upper case to lower case does not get flagged as a change so adding a `_` to make the switch to lower case for notebook 1
- also add placeholder doi link for pub

* finish notebook name changes (for now)

data/experimental_parameters.json

@@ -0,0 +1,78 @@
+{
+    "AMID-04": {
+        "S1-Cr3-T": {
+            "strain": "cc124",
+            "vessel_type": "pools",
+            "position_in_tube": "top",
+            "time_in_water": 21
+        },
+        "S2-Cr3-M": {
+            "strain": "cc124",
+            "vessel_type": "pools",
+            "position_in_tube": "middle",
+            "time_in_water": 21
+        },
+        "S3-Cr4-T": {
+            "strain": "cc124",
+            "vessel_type": "pools",
+            "position_in_tube": "top",
+            "time_in_water": 4
+        },
+        "S4-Cr4-M": {
+            "strain": "cc124",
+            "vessel_type": "pools",
+            "position_in_tube": "middle",
+            "time_in_water": 4
+        }
+    },
+    "AMID-05": {
+        "I01": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "top",
+            "time_in_water": 21
+        },
+        "J01": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "top",
+            "time_in_water": 21
+        },
+        "K01": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "top",
+            "time_in_water": 4
+        },
+        "L01": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "top",
+            "time_in_water": 4
+        },
+        "I03": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "middle",
+            "time_in_water": 21
+        },
+        "J03": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "middle",
+            "time_in_water": 21
+        },
+        "K03": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "middle",
+            "time_in_water": 4
+        },
+        "L03": {
+            "strain": "cc124",
+            "vessel_type": "wells",
+            "position_in_tube": "middle",
+            "time_in_water": 4
+        }
+    }
+}