Skip to content

Heatmap Report Enhancements #93

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
davewalker5 merged 1 commit into from
Apr 17, 2025
Merged

Heatmap Report Enhancements #93

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
57 changes: 44 additions & 13 deletions reports/heatmap.ipynb → ...ts/annual_category_location_heatmap.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,11 @@
"# Species category to report on\n",
"category = \"\"\n",
"\n",
"# Export format - either PNG or PDF\n",
"export_format = \"PNG\""
"# Export format for the heatmap chart:\n",
"# PNG - export as PNG image\n",
"# PDF - export as PDF file\n",
"# <blank> - do not export\n",
"export_format = \"\""
]
},
{
Expand Down Expand Up @@ -65,7 +68,12 @@
"# Connect to the database, execute the query and read the results into a dataframe\n",
"database_path = os.environ[\"NATURE_RECORDER_DB\"]\n",
"connection = sqlite3.connect(database_path)\n",
"df = pd.read_sql_query(query, connection, parse_dates=[\"Date\"])"
"df = pd.read_sql_query(query, connection, parse_dates=[\"Date\"])\n",
"\n",
"# Check there is some data\n",
"if not df.shape[0]:\n",
" message = f\"No data found for category '{category}' at location '{location}' during '{year}'\"\n",
" raise ValueError(message)"
]
},
{
Expand All @@ -76,11 +84,38 @@
"outputs": [],
"source": [
"import calendar\n",
"import re\n",
"\n",
"# Create the folder to hold exported reports\n",
"export_folder_path = Path(\"exported\")\n",
"export_folder_path.mkdir(parents=True, exist_ok=True)\n",
"\n",
"# Pre-process the data to provide a heatmap data source\n",
"df[\"Month\"] = df[\"Date\"].dt.month\n",
"heatmap_data = df.groupby([\"Species\", \"Month\"]).size().unstack(fill_value=0)\n",
"heatmap_data.columns = [calendar.month_abbr[m] for m in heatmap_data.columns]"
"heatmap_data = df.groupby([\"Species\", \"Month\"])[\"Count\"].sum().unstack(fill_value=0)\n",
"\n",
"# Make sure all months are represented even if there are no sightings in the data set for that month\n",
"for month in range(1, 13):\n",
" if month not in heatmap_data.columns:\n",
" heatmap_data[month] = 0\n",
"\n",
"# Re-order the columns in calendar order\n",
"heatmap_data = heatmap_data[sorted(heatmap_data.columns)]\n",
"\n",
"# Set the labels to the month abbreviations rather than month numbers\n",
"heatmap_data.columns = [calendar.month_abbr[m] for m in heatmap_data.columns]\n",
"\n",
"# Export the heatmap data to Excel\n",
"clean_location = re.sub(\"[^0-9a-zA-Z\\-]+\", \"\", location.replace(\" \", \"-\"))\n",
"export_file_path = export_folder_path / f\"{year}-{category}-{clean_location}-Heatmap.xlsx\"\n",
"heatmap_data.to_excel(export_file_path.absolute(), sheet_name=\"Sightings\")\n",
"\n",
"# Print the heatmap data\n",
"with pd.option_context('display.max_rows', None,\n",
" 'display.max_columns', None,\n",
" 'display.precision', 3,\n",
" ):\n",
" display(heatmap_data)"
]
},
{
Expand All @@ -94,24 +129,20 @@
"import matplotlib.pyplot as plt\n",
"\n",
"# Generate the heatmap\n",
"plt.figure(figsize=(12, 24))\n",
"plt.figure(figsize=(12, heatmap_data.shape[0] / 3))\n",
"sns.heatmap(heatmap_data, cmap=\"YlOrRd\", annot=False)\n",
"plt.title(f\"Number of Sightings of {category} at {location} in {year}\")\n",
"plt.xlabel(\"\")\n",
"plt.ylabel(\"\")\n",
"\n",
"# Create the folder to hold exported reports\n",
"export_folder_path = Path(\"exported\")\n",
"export_folder_path.mkdir(parents=True, exist_ok=True)\n",
"\n",
"# Export to PNG\n",
"if export_format.casefold() == \"png\":\n",
" export_file_path = export_folder_path / f\"{year}-{category}-Heatmap.png\"\n",
" export_file_path = export_folder_path / f\"{year}-{category}-{clean_location}-Heatmap.png\"\n",
" plt.savefig(export_file_path.absolute(), format=\"png\", dpi=300, bbox_inches=\"tight\")\n",
"\n",
"# Export to PDF\n",
"if export_format.casefold() == \"pdf\":\n",
" export_file_path = Path(\"exported\") / f\"{year}-{category}-Heatmap.pdf\"\n",
" export_file_path = export_folder_path / f\"{year}-{category}-{clean_location}-Heatmap.pdf\"\n",
" plt.savefig(export_file_path.absolute(), format=\"pdf\", bbox_inches=\"tight\")\n",
"\n",
"# And show the plot\n",
Expand All @@ -121,7 +152,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "venv",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand Down
2 changes: 2 additions & 0 deletions reports/requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ cycler==0.12.1
debugpy==1.8.14
decorator==5.2.1
defusedxml==0.7.1
et_xmlfile==2.0.0
executing==2.2.0
fastjsonschema==2.21.1
fonttools==4.57.0
Expand Down Expand Up @@ -61,6 +62,7 @@ nest-asyncio==1.6.0
notebook==7.4.0
notebook_shim==0.2.4
numpy==2.2.4
openpyxl==3.1.5
overrides==7.7.0
packaging==24.2
pandas==2.2.3
Expand Down
4 changes: 2 additions & 2 deletions reports/sql/sightings.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
SELECT l.Name AS 'Location', sp.Name AS 'Species', sp.Name AS 'Category', DATE( s.Date ) AS 'Date'
SELECT l.Name AS 'Location', sp.Name AS 'Species', sp.Name AS 'Category', DATE( s.Date ) AS 'Date', IFNULL( s.Number, 1 ) AS 'Count'
FROM SIGHTINGS s
INNER JOIN SPECIES sp ON sp.Id = s.SpeciesId
INNER JOIN CATEGORIES c ON c.Id = sp.CategoryId
INNER JOIN LOCATIONS l ON l.Id = s.LocationId
WHERE l.Name = '$LOCATION'
AND s.Date LIKE '$YEAR-%'
AND sp.Name LIKE '%$SPECIES%'
AND c.Name = "$CATEGORY";
AND c.Name = "$CATEGORY";