mega rerun everything

neurodata · May 19, 2022 · 7955195 · 7955195
1 parent 3dad199
commit 7955195
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Showing 30 changed files with 2,658 additions and 2,631 deletions.
diff --git a/docs/connectomes.ipynb b/docs/connectomes.ipynb
diff --git a/docs/explain.ipynb b/docs/explain.ipynb
diff --git a/docs/process_c_elegans.ipynb b/docs/process_c_elegans.ipynb
diff --git a/docs/process_maggot.ipynb b/docs/process_maggot.ipynb
diff --git a/docs/process_p_pacificus.ipynb b/docs/process_p_pacificus.ipynb
diff --git a/docs/simulations.ipynb b/docs/simulations.ipynb
diff --git a/overleaf b/overleaf
diff --git a/pkg/pkg/data/__init__.py b/pkg/pkg/data/__init__.py
@@ -1 +1 @@
-from .load_data import DATA_PATH, DATA_VERSION, load_split_connectome
+from .load_data import DATA_PATH, load_split_connectome
diff --git a/pkg/pkg/data/load_data.py b/pkg/pkg/data/load_data.py
@@ -4,28 +4,10 @@
 import pandas as pd
 
 
-version_loc = Path(__file__).parent / "version.txt"
-with open(version_loc) as f:
-    version = f.readline()
-
-processed_loc = Path(__file__).parent / "processed_version.txt"
-with open(processed_loc) as f:
-    processed_version = f.readline()
-
-DATA_VERSION = version
 DATA_PATH = Path(__file__).parent.parent.parent.parent  # don't judge me judge judy
 DATA_PATH = DATA_PATH / "data"
 
 
-def _get_folder(path, version):
-    if path is None:
-        path = DATA_PATH
-    if version is None:
-        version = DATA_VERSION
-    folder = path / version
-    return folder
-
-
 def load_split_connectome(dataset, weights=True):
     dir = DATA_PATH / "processed_split"
     if weights:

diff --git a/pkg/pkg/match/solver.py b/pkg/pkg/match/solver.py
@@ -18,7 +18,9 @@
 # Type aliases
 PaddingType = Literal["adopted", "naive"]
 InitMethodType = Literal["barycenter", "rand", "randomized"]
-RandomStateType = Optional[Union[int, np.random.RandomState, np.random.Generator]]
+RandomStateType = Optional[
+    Union[int, np.random.RandomState, np.random.Generator, np.integer]
+]
 ArrayLikeOfIndexes = Union[List[int], np.ndarray]
 MultilayerAdjacency = Union[List[AdjacencyMatrix], AdjacencyMatrix, np.ndarray]
 Scalar = Union[int, float, np.integer]

diff --git a/pkg/pkg/plot/__init__.py b/pkg/pkg/plot/__init__.py
@@ -8,6 +8,7 @@
     get_text_width,
     get_texts_points,
     make_sequential_colormap,
+    merge_axes,
     multicolor_text,
     nice_text,
     rainbowarrow,

diff --git a/pkg/pkg/plot/utils.py b/pkg/pkg/plot/utils.py
@@ -232,3 +232,27 @@ def rainbowarrow(ax, start, end, cmap="viridis", n=50, lw=3):
     tri = mpl.path.Path(tricoords2, closed=True)
     ax.scatter(end[0], end[1], c=1, s=(2 * lw) ** 2, marker=tri, cmap=cmap, vmin=0)
     ax.autoscale_view()
+
+
+def _get_slice(items, n_items):
+    if items is None:
+        return slice(0, n_items)
+    elif type(items) == int:
+        return items
+    elif len(items) == 1:
+        return items[0]
+    else:
+        return slice(items[0], items[1])
+
+
+def merge_axes(fig, axs, rows=None, cols=None):
+    # TODO I could't figure out a safer way to do this without eval
+    # seems like gridspec.__getitem__ only wants numpy indices in the slicing form
+    # REF: https://matplotlib.org/stable/gallery/subplots_axes_and_figures/gridspec_and_subplots.html
+    row_slice = _get_slice(rows, axs.shape[0])
+    col_slice = _get_slice(cols, axs.shape[1])
+    gs = axs.flat[0].get_gridspec()
+    for ax in axs[row_slice, col_slice].ravel():
+        ax.remove()
+    ax = fig.add_subplot(gs[row_slice, col_slice])
+    return ax
diff --git a/pkg/pkg/utils/__init__.py b/pkg/pkg/utils/__init__.py
@@ -1,5 +1,4 @@
 from .toy import get_toy_palette, sample_toy_networks
-from .utils import set_warnings
 from .wrangle import (
     create_node_data,
     ensure_connected,

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -11,6 +11,7 @@ graspologic = "^1.0.0"
 jupyter-client = "6.1.12" # https://github.com/jupyter/jupyter_client/issues/637
 svgutils = "^0.3.4"
 python-catmaid = "^2.1.1"
+jupytext = "^1.13.8"
 
 [tool.poetry.dev-dependencies]
 black = "^22.3.0"

diff --git a/results/figs/connectomes/match_accuracy_comparison.pdf b/results/figs/connectomes/match_accuracy_comparison.pdf
diff --git a/results/figs/connectomes/match_accuracy_comparison.png b/results/figs/connectomes/match_accuracy_comparison.png