foo:
This commit is contained in:
Felix Delattre
parent
fa59122e3b
commit
5ceeeabd11
9 changed files with 110 additions and 37 deletions
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@ -148,21 +148,46 @@ def calculate_phenocam_stats(phenocam_ts):
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}
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def _s2_kept_date_set(base: Path, strategy: str) -> set:
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def _s2_gcc_series_from_preselection(base: Path):
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"""Build the raw S2 GCC series from s2_preselection.json.
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Uses the 3x3 site-window band means stored per raw S2 acquisition and
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computes GCC = b03 / (b02 + b03 + b04). Scale cancels, so DN vs
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reflectance is irrelevant. Returns (all_gcc, flags) where all_gcc maps
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YYYY-MM-DD -> gcc for every row with a positive band sum, and flags maps
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the same date key -> (excluded_aggressive, excluded_nonaggressive).
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"""
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path = base / "raw" / "preselection" / "s2_preselection.json"
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if not path.exists():
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return set()
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return {}, {}
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with open(path) as f:
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rows = json.load(f)
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key = f"excluded_{strategy}"
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out = set()
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all_gcc: dict = {}
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flags: dict = {}
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for e in rows:
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if e.get(key):
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continue
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nk = _norm_date_key(e.get("date"))
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if nk:
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out.add(nk)
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return out
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if not nk:
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continue
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try:
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b02 = float(e.get("b02"))
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b03 = float(e.get("b03"))
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b04 = float(e.get("b04"))
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except (TypeError, ValueError):
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continue
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total = b02 + b03 + b04
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if not np.isfinite(total) or total <= 0:
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continue
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gcc = b03 / total
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if not np.isfinite(gcc):
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continue
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if nk in all_gcc:
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continue
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all_gcc[nk] = float(gcc)
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flags[nk] = (
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bool(e.get("excluded_aggressive")),
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bool(e.get("excluded_nonaggressive")),
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)
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return all_gcc, flags
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def _whittaker_smooth_dict(obs_dates, obs_values, lam: float, n_min: int = 3):
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@ -221,33 +246,27 @@ def calculate_all_metrics(season, site_name, site_position):
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results["phenocam_stats"] = phenocam_stats
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baseline = {}
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s2_ts = {}
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for sub in ("processed_aggressive_sigma20", "processed_nonaggressive_sigma20"):
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p = base / sub / "gcc" / "s2" / "timeseries.json"
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if p.exists():
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s2_ts = load_timeseries(p)
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if s2_ts:
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break
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if s2_ts:
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m0 = calculate_temporal_metrics(s2_ts, phenocam_ts)
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all_gcc, flags = _s2_gcc_series_from_preselection(base)
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if all_gcc:
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m0 = calculate_temporal_metrics(all_gcc, phenocam_ts)
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if m0:
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baseline["s2"] = m0
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for strategy in ("aggressive", "nonaggressive"):
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kept = _s2_kept_date_set(base, strategy)
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filtered = [
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(k, v)
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for k, v in sorted(
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s2_ts.items(), key=lambda x: _norm_date_key(x[0]) or ""
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for strategy, flag_idx in (("aggressive", 0), ("nonaggressive", 1)):
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kept_items = sorted(
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(
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(d, g)
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for d, g in all_gcc.items()
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if d in flags and not flags[d][flag_idx]
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),
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key=lambda x: x[0],
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)
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if _norm_date_key(k) in kept and v is not None
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]
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if not filtered:
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if not kept_items:
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continue
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sub_ts = dict(filtered)
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mcf = calculate_temporal_metrics(sub_ts, phenocam_ts)
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kept_ts = dict(kept_items)
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mcf = calculate_temporal_metrics(kept_ts, phenocam_ts)
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if mcf:
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baseline.setdefault("s2_cloudfree", {})[strategy] = mcf
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obs_d, obs_v = zip(*filtered)
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obs_d, obs_v = zip(*kept_items)
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smooth = _whittaker_smooth_dict(obs_d, obs_v, WHITTAKER_LAMBDA_DAYS_SQ)
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if smooth:
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mw = calculate_temporal_metrics(smooth, phenocam_ts)
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@ -4,6 +4,7 @@ openeo
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python-dotenv
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netCDF4
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numpy
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timesat
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requests
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scipy
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matplotlib
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4
run.py
4
run.py
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@ -17,6 +17,7 @@ from preparation import (
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)
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from metrics_indices import create_prepared_fusion_timeseries
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from metrics_stats import calculate_all_metrics
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from phenology_timesat import write_phenocam_phenology_for_site
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def run_pipeline(season, site_position, site_name):
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@ -27,6 +28,9 @@ def run_pipeline(season, site_position, site_name):
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# download_s3(season, site_position, site_name)
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# download_phenocam(season, site_position, site_name)
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print(f"PhenoCam phenology (50 % amplitude): {site_name}, {season}")
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write_phenocam_phenology_for_site(site_name, season)
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print(f"Creating preselection timeseries: {site_name}, {season}")
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create_timeseries(season, site_position, site_name)
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@ -44,6 +44,7 @@
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<a href="fusion.html" class="active">Fusion</a>
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<a href="postprocessed.html">Postprocessed</a>
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<a href="metrics.html">Metrics</a>
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<a href="phenology.html">Phenology</a>
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</div>
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<h1 id="siteName">Innsbruck</h1>
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<div class="season-row"><h2 id="season">2024</h2><span class="download-links" id="downloadLinks"></span></div>
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@ -25,6 +25,7 @@
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.site-info h2 { margin: 0 0 20px 0; font-size: 18px; color: #666; }
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.phenocam-label { font-size: 12px; margin-bottom: 5px; color: #666; }
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.phenocam-date { font-size: 11px; margin-top: 5px; color: #999; }
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.timeseries-phenology { font-size: 11px; color: #444; line-height: 1.45; margin-top: 6px; white-space: pre-line; }
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.phenocam-image { width: 100%; height: 200px; object-fit: contain; border: 1px solid #ccc; }
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.sitemap { height: 200px; border: 1px solid #ccc; margin-top: 32px; }
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#greennesstimeseries { margin-top: 0; }
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@ -54,6 +55,7 @@
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<a href="fusion.html">Fusion</a>
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<a href="postprocessed.html">Postprocessed</a>
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<a href="metrics.html">Metrics</a>
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<a href="phenology.html">Phenology</a>
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</div>
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<div class="slider-container">
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<input type="range" id="dateSlider" min="0" max="365" value="0">
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@ -70,6 +72,7 @@
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<div class="header-col">
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<div class="timeseries-label">Greenness Index Timeseries</div>
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<canvas id="greennesstimeseries" class="timeseries"></canvas>
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<div id="phenocamPhenology" class="timeseries-phenology"></div>
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</div>
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<div class="header-col">
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<div id="sitemap" class="sitemap"></div>
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@ -172,6 +175,8 @@
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let timeseries = { s2: [], fusion: [], s3: [] };
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let greennessTimeseries = { s2: [], fusion: [], s3: [] };
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let phenocamGreennessTimeseries = [];
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/** @type {{ green_up_50pct_date: string | null, green_down_50pct_date: string | null } | null} */
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let phenocamPhenology = null;
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// Add site marker to all maps
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for (const source of ["s2", "fusion", "s3"]) {
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@ -180,6 +185,39 @@
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let syncing = false;
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const allMaps = Object.values(maps);
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function updatePhenocamPhenologyText() {
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const el = document.getElementById("phenocamPhenology");
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if (!el) return;
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if (!phenocamPhenology || (phenocamPhenology.green_up_50pct_date == null && phenocamPhenology.green_down_50pct_date == null)) {
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el.textContent = "";
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return;
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}
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const up = phenocamPhenology.green_up_50pct_date || "—";
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const dn = phenocamPhenology.green_down_50pct_date || "—";
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el.textContent = `* Green-up: ${up}\n* Green-down: ${dn}`;
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}
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const PHENOLOGY_VLINE = "rgba(150, 200, 255, 0.95)";
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function strokePhenologyVlines(ctx, minDate, maxDate, dateRange, plotW, pad, plotH) {
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if (!phenocamPhenology) return;
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for (const iso of [phenocamPhenology.green_up_50pct_date, phenocamPhenology.green_down_50pct_date]) {
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if (!iso) continue;
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const d = new Date(iso);
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if (isNaN(d.getTime()) || d < minDate || d > maxDate) continue;
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const px = pad + ((d - minDate) / dateRange) * plotW;
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ctx.save();
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ctx.setLineDash([4, 3]);
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ctx.strokeStyle = PHENOLOGY_VLINE;
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ctx.lineWidth = 1.5;
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ctx.beginPath();
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ctx.moveTo(px, pad);
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ctx.lineTo(px, pad + plotH);
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ctx.stroke();
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ctx.restore();
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}
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}
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const syncMaps = (sourceMap) => {
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if (syncing) return;
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syncing = true;
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@ -197,18 +235,21 @@
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async function loadTimeseries() {
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metricsData = null;
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const fusionPath = getFusionPath();
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const [s2, fusion, s3, s2gcc, fusiongcc, s3gcc, phenocam] = await Promise.all([
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const [s2, fusion, s3, s2gcc, fusiongcc, s3gcc, phenocam, phenPhen] = await Promise.all([
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fetch(`data/${siteName}/${season}/processed_${strategy}_sigma${sigma}/ndvi/s2/timeseries.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/${fusionPath}/ndvi/fusion/timeseries.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/processed_${strategy}_sigma${sigma}/ndvi/s3/timeseries.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/processed_${strategy}_sigma${sigma}/gcc/s2/timeseries.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/${fusionPath}/gcc/fusion/timeseries.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/processed_${strategy}_sigma${sigma}/gcc/s3/timeseries.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/raw/phenocam/phenocam_gcc.json`).then(r => r.json()).catch(() => [])
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fetch(`data/${siteName}/${season}/raw/phenocam/phenocam_gcc.json`).then(r => r.json()).catch(() => []),
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fetch(`data/${siteName}/${season}/raw/phenocam/phenocam_phenology.json`).then(r => r.ok ? r.json() : null).catch(() => null)
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]);
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timeseries = { s2, fusion, s3 };
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greennessTimeseries = { s2: s2gcc, fusion: fusiongcc, s3: s3gcc };
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phenocamGreennessTimeseries = phenocam;
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phenocamPhenology = phenPhen && (phenPhen.green_up_50pct_date != null || phenPhen.green_down_50pct_date != null) ? phenPhen : null;
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updatePhenocamPhenologyText();
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// Load all scenario GCC timeseries for comparison
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const scenarios = [
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@ -289,10 +330,11 @@
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ctx.fillStyle = "#888";
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const axisY = pad + plotH;
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for (const t of data) ctx.fillRect(x(t.date) - 1, axisY - 1, 2, 2);
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strokePhenologyVlines(ctx, minDate, maxDate, dateRange, plotW, pad, plotH);
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const xPos = x(currentDate);
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ctx.strokeStyle = "#f00";
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ctx.lineWidth = 2;
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ctx.setLineDash([]);
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ctx.beginPath();
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ctx.moveTo(xPos, pad);
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ctx.lineTo(xPos, pad + plotH);
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@ -360,11 +402,12 @@
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ctx.fillStyle = "#888";
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const axisY = pad + plotH;
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for (const t of data) ctx.fillRect(x(t.date) - 1, axisY - 1, 2, 2);
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strokePhenologyVlines(ctx, minDate, maxDate, dateRange, plotW, pad, plotH);
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const currentDate = dateFromDays(parseInt(slider.value));
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const xPos = x(currentDate);
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ctx.strokeStyle = "#f00";
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ctx.lineWidth = 2;
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ctx.setLineDash([]);
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ctx.beginPath();
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ctx.moveTo(xPos, pad);
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ctx.lineTo(xPos, pad + plotH);
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@ -460,17 +503,17 @@
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ctx.fillStyle = "#888";
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const axisY = pad + plotH;
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for (const t of [...s2data, ...fusiondata, ...phenocamdata]) ctx.fillRect(x(t.date) - 1, axisY - 1, 2, 2);
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strokePhenologyVlines(ctx, minDate, maxDate, dateRange, plotW, pad, plotH);
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const legendX = pad + plotW - 80, legendY = pad + 5;
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ctx.font = "9px sans-serif";
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if (s2data.length) { ctx.strokeStyle = "#ff6600"; ctx.beginPath(); ctx.moveTo(legendX, legendY); ctx.lineTo(legendX + 15, legendY); ctx.stroke(); ctx.fillStyle = "#000"; ctx.fillText("S2", legendX + 18, legendY + 3); }
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if (fusiondata.length) { ctx.strokeStyle = "#9900cc"; ctx.beginPath(); ctx.moveTo(legendX, legendY + 12); ctx.lineTo(legendX + 15, legendY + 12); ctx.stroke(); ctx.fillStyle = "#000"; ctx.fillText("Fusion", legendX + 18, legendY + 15); }
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if (phenocamdata.length) { ctx.strokeStyle = "#00aa00"; ctx.beginPath(); ctx.moveTo(legendX, legendY + 24); ctx.lineTo(legendX + 15, legendY + 24); ctx.stroke(); ctx.fillStyle = "#000"; ctx.fillText("PhenoCam", legendX + 18, legendY + 27); }
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const currentDate = dateFromDays(parseInt(slider.value));
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const xPos = x(currentDate);
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ctx.strokeStyle = "#f00";
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ctx.lineWidth = 2;
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ctx.setLineDash([]);
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ctx.beginPath();
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ctx.moveTo(xPos, pad);
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ctx.lineTo(xPos, pad + plotH);
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@ -545,6 +588,7 @@
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ctx.fillText(name, legendX + 18, legendY + i * 12 + 3);
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}
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});
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strokePhenologyVlines(ctx, minDate, maxDate, dateRange, plotW, pad, plotH);
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}
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function drawMetricsTable() {
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@ -38,6 +38,7 @@
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<a href="fusion.html">Fusion</a>
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<a href="postprocessed.html">Postprocessed</a>
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<a href="metrics.html" class="active">Metrics</a>
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<a href="phenology.html">Phenology</a>
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</div>
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<h1 id="siteName">Metrics</h1>
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<div class="selectors">
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@ -44,6 +44,7 @@
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<a href="fusion.html">Fusion</a>
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<a href="postprocessed.html" class="active">Postprocessed</a>
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<a href="metrics.html">Metrics</a>
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<a href="phenology.html">Phenology</a>
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</div>
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<h1 id="siteName">Innsbruck</h1>
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<div class="season-row"><h2 id="season">2024</h2><span class="download-links" id="downloadLinks"></span></div>
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@ -44,6 +44,7 @@
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<a href="fusion.html">Fusion</a>
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<a href="postprocessed.html">Postprocessed</a>
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<a href="metrics.html">Metrics</a>
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<a href="phenology.html">Phenology</a>
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</div>
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<h1 id="siteName">Innsbruck</h1>
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<div class="season-row"><h2 id="season">2024</h2><span class="download-links" id="downloadLinks"></span></div>
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@ -43,6 +43,7 @@
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<a href="fusion.html">Fusion</a>
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<a href="postprocessed.html">Postprocessed</a>
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<a href="metrics.html">Metrics</a>
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<a href="phenology.html">Phenology</a>
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</div>
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<h1 id="siteName">Innsbruck</h1>
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<div class="season-row"><h2 id="season">2024</h2><span class="download-links" id="downloadLinks"></span></div>
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