egrace479 commited on
Commit
8922683
1 Parent(s): 3264ec4

Remove "-" causing problems with dataset viewer (#8)

Browse files

- update lfs tracking in gitattributes (929680d0ec74222a0d89f842a6cdcad422434b69)
- Replace '-' in 'Collected_by' column to fix dataset viewer rendering (03f93bf7afdab95e7c67e49f13d4a8a6f6f205ee)
- Notebook finding and fixing the '-' in 'Collected_by' column of full and heliconius CSVs (d65770f7a85dae010c6ebfc9592567f472c25ef6)

.gitattributes CHANGED
@@ -55,8 +55,11 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  *.webp filter=lfs diff=lfs merge=lfs -text
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  # Large CSVs
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- Jiggins_Zenodo_Img_Master.csv filter=lfs diff=lfs merge=lfs -text
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- Jiggins_Heliconius_Master.csv filter=lfs diff=lfs merge=lfs -text
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  metadata/Jiggins_Zenodo_Master.csv filter=lfs diff=lfs merge=lfs -text
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  deduplication_process/Jiggins_Zenodo_Img_Master_3477891Patch.csv filter=lfs diff=lfs merge=lfs -text
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  deduplication_process/metadata/Jiggins_Zenodo_Img_Master_3477891Patch_downloaded.csv filter=lfs diff=lfs merge=lfs -text
 
 
 
 
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  *.webp filter=lfs diff=lfs merge=lfs -text
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  # Large CSVs
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+ img_master.csv filter=lfs diff=lfs merge=lfs -text
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+ Heliconius_img_master.csv filter=lfs diff=lfs merge=lfs -text
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  metadata/Jiggins_Zenodo_Master.csv filter=lfs diff=lfs merge=lfs -text
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  deduplication_process/Jiggins_Zenodo_Img_Master_3477891Patch.csv filter=lfs diff=lfs merge=lfs -text
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  deduplication_process/metadata/Jiggins_Zenodo_Img_Master_3477891Patch_downloaded.csv filter=lfs diff=lfs merge=lfs -text
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+ #older copies:
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+ Jiggins_Zenodo_Img_Master.csv filter=lfs diff=lfs merge=lfs -text
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+ Jiggins_Heliconius_Master.csv filter=lfs diff=lfs merge=lfs -text
Heliconius_img_master.csv CHANGED
@@ -1,3 +1,3 @@
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  version https://git-lfs.github.com/spec/v1
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- oid sha256:e61a7a3b58ba98221b2a79e4b8749d5283fe652cf007a01557b795280c99612c
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- size 13683618
 
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  version https://git-lfs.github.com/spec/v1
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+ oid sha256:a0c3cedf2f8eaeab9763f333a69e157753085a9f3e979b9e49147e895c3427f0
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+ size 13683556
img_master.csv CHANGED
@@ -1,3 +1,3 @@
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  version https://git-lfs.github.com/spec/v1
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- oid sha256:1a82068174884a3663609248aff77c0f292c922582a2a5c7b03b4201489b20fd
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- size 16639783
 
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  version https://git-lfs.github.com/spec/v1
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+ oid sha256:a0018cb09605ab1eb1ecbfd8dbe631537ea0d3ac6da28afe2e7a2ee897b4113f
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+ size 16639721
notebooks/Data-gen-1-4.ipynb ADDED
@@ -0,0 +1,136 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ {
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+ "cells": [
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+ {
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+ "cell_type": "code",
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+ "execution_count": 1,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "import pandas as pd\n",
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+ "import numpy as np"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "# Fix \"-\" in \"Collected_by\" Columns in full_master and Heliconius subsets\n",
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+ "\n",
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+ "See [discussion](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly/discussions/7). I then tested each column that showed up as \"null\" in type on the dataset viewer (searching for df[col] == \"-\")."
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 2,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# while main is commit 3264ec40dbc9db025e027ddb2abca0914cd6500f\n",
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+ "df = pd.read_csv(\"https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly/resolve/main/img_master.csv\", low_memory= False)\n",
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+ "df_heli = pd.read_csv(\"https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly/resolve/main/Heliconius_img_master.csv\", low_memory=False)"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 3,
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "column Collected_by has 62 instances of '-'\n"
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+ ]
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+ }
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+ ],
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+ "source": [
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+ "for col in list(df.columns):\n",
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+ " temp = df.loc[df[col] == \"-\"]\n",
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+ " if temp.shape[0] > 0:\n",
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+ " print(f\"column {col} has {temp.shape[0]} instances of '-'\")"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 4,
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "column Collected_by has 62 instances of '-'\n"
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+ ]
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+ }
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+ ],
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+ "source": [
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+ "for col in list(df_heli.columns):\n",
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+ " temp = df_heli.loc[df_heli[col] == \"-\"]\n",
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+ " if temp.shape[0] > 0:\n",
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+ " print(f\"column {col} has {temp.shape[0]} instances of '-'\")"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "Looks like we just need to fix the `Collected_by` column for both CSVs. We'll replace these with `null` so that it doesn't break the dataset viewer."
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 5,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "df.loc[df[\"Collected_by\"] == \"-\", \"Collected_by\"] = np.nan\n",
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+ "df_heli.loc[df_heli[\"Collected_by\"] == \"-\", \"Collected_by\"] = np.nan"
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+ ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "## Now let's save the fix"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 6,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "df.to_csv(\"../img_master.csv\", index = False)\n",
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+ "df_heli.to_csv(\"../Heliconius_img_master.csv\", index = False)"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": []
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+ }
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+ ],
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+ "metadata": {
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+ "kernelspec": {
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+ "display_name": "std",
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+ "language": "python",
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+ "name": "python3"
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+ },
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+ "language_info": {
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+ "codemirror_mode": {
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+ "name": "ipython",
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+ "version": 3
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+ },
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+ "file_extension": ".py",
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+ "mimetype": "text/x-python",
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+ "name": "python",
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+ "nbconvert_exporter": "python",
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+ "pygments_lexer": "ipython3",
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+ "version": "3.11.3"
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+ }
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+ },
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+ "nbformat": 4,
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+ "nbformat_minor": 2
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+ }