From 2f9fa3b1a7fe4bebce8ce8726bcc39f5bf4f1261 Mon Sep 17 00:00:00 2001
From: Shumpei Shiina <s417.lama@gmail.com>
Date: Tue, 15 Oct 2019 23:14:02 -0500
Subject: [PATCH 1/5] Fix width of box plots with log-scale axis

---
 src/plots/cartesian/autorange.js       |  29 +++++---
 src/traces/box/cross_trace_calc.js     |   4 +-
 src/traces/box/hover.js                |   2 +-
 src/traces/box/plot.js                 |  27 +++----
 test/image/baselines/box_log_scale.png | Bin 0 -> 16324 bytes
 test/image/mocks/box_log_scale.json    |  94 +++++++++++++++++++++++++
 6 files changed, 130 insertions(+), 26 deletions(-)
 create mode 100644 test/image/baselines/box_log_scale.png
 create mode 100644 test/image/mocks/box_log_scale.json

diff --git a/src/plots/cartesian/autorange.js b/src/plots/cartesian/autorange.js
index 2b8a176d747..ca3b16805cb 100644
--- a/src/plots/cartesian/autorange.js
+++ b/src/plots/cartesian/autorange.js
@@ -298,6 +298,8 @@ function doAutoRange(gd, ax) {
  *          (unless one end is overridden by tozero)
  *      tozero: (boolean) make sure to include zero if axis is linear,
  *          and make it a tight bound if possible
+ *      vpadLinearized: (boolean) whether or not vpad (or vpadplus/vpadminus)
+ *          is linearized (for log scale axes)
  *
  * @return {object}
  *  - min {array of objects}
@@ -320,6 +322,7 @@ function findExtremes(ax, data, opts) {
     var tozero = opts.tozero && (ax.type === 'linear' || ax.type === '-');
     var isLog = ax.type === 'log';
     var hasArrayOption = false;
+    var vpadLinearized = opts.vpadLinearized || false;
     var i, v, di, dmin, dmax, ppadiplus, ppadiminus, vmin, vmax;
 
     function makePadAccessor(item) {
@@ -371,16 +374,22 @@ function findExtremes(ax, data, opts) {
         if(!isNumeric(di)) return;
         ppadiplus = ppadplus(i);
         ppadiminus = ppadminus(i);
-        vmin = di - vpadminus(i);
-        vmax = di + vpadplus(i);
-        // special case for log axes: if vpad makes this object span
-        // more than an order of mag, clip it to one order. This is so
-        // we don't have non-positive errors or absurdly large lower
-        // range due to rounding errors
-        if(isLog && vmin < vmax / 10) vmin = vmax / 10;
-
-        dmin = ax.c2l(vmin);
-        dmax = ax.c2l(vmax);
+
+        if(vpadLinearized) {
+            dmin = ax.c2l(di) - vpadminus(i);
+            dmax = ax.c2l(di) + vpadplus(i);
+        } else {
+            vmin = di - vpadminus(i);
+            vmax = di + vpadplus(i);
+            // special case for log axes: if vpad makes this object span
+            // more than an order of mag, clip it to one order. This is so
+            // we don't have non-positive errors or absurdly large lower
+            // range due to rounding errors
+            // if(isLog && vmin < vmax / 10) vmin = vmax / 10;
+
+            dmin = ax.c2l(vmin);
+            dmax = ax.c2l(vmax);
+        }
 
         if(tozero) {
             dmin = Math.min(0, dmin);
diff --git a/src/traces/box/cross_trace_calc.js b/src/traces/box/cross_trace_calc.js
index a13f701c47b..b1792cb9794 100644
--- a/src/traces/box/cross_trace_calc.js
+++ b/src/traces/box/cross_trace_calc.js
@@ -60,7 +60,7 @@ function setPositionOffset(traceType, gd, boxList, posAxis) {
     for(i = 0; i < boxList.length; i++) {
         calcTrace = calcdata[boxList[i]];
         for(j = 0; j < calcTrace.length; j++) {
-            pointList.push(calcTrace[j].pos);
+            pointList.push(posAxis.c2l(calcTrace[j].pos, true));
             shownPts += (calcTrace[j].pts2 || []).length;
         }
     }
@@ -125,7 +125,6 @@ function setPositionOffset(traceType, gd, boxList, posAxis) {
         t.bPos = bPos;
         t.bdPos = bdPos;
         t.wHover = wHover;
-
         // box/violin-only value-space push value
         var pushplus;
         var pushminus;
@@ -213,6 +212,7 @@ function setPositionOffset(traceType, gd, boxList, posAxis) {
             padded: padded,
             vpadminus: vpadminus,
             vpadplus: vpadplus,
+            vpadLinearized: true,
             // N.B. SVG px-space positive/negative
             ppadminus: {x: ppadminus, y: ppadplus}[axLetter],
             ppadplus: {x: ppadplus, y: ppadminus}[axLetter],
diff --git a/src/traces/box/hover.js b/src/traces/box/hover.js
index 0eac65f7669..8e40188841b 100644
--- a/src/traces/box/hover.js
+++ b/src/traces/box/hover.js
@@ -60,7 +60,7 @@ function hoverOnBoxes(pointData, xval, yval, hovermode) {
     var boxDelta = t.bdPos;
     var boxDeltaPos, boxDeltaNeg;
     var posAcceptance = t.wHover;
-    var shiftPos = function(di) { return di.pos + t.bPos - pVal; };
+    var shiftPos = function(di) { return pAxis.c2l(di.pos) + t.bPos - pAxis.c2l(pVal); };
 
     if(isViolin && trace.side !== 'both') {
         if(trace.side === 'positive') {
diff --git a/src/traces/box/plot.js b/src/traces/box/plot.js
index 3a1eefdfa85..1f6d3432c66 100644
--- a/src/traces/box/plot.js
+++ b/src/traces/box/plot.js
@@ -86,16 +86,16 @@ function plotBoxAndWhiskers(sel, axes, trace, t) {
     paths.each(function(d) {
         if(d.empty) return 'M0,0Z';
 
-        var pos = d.pos;
-        var posc = posAxis.c2p(pos + bPos, true) + bPosPxOffset;
-        var pos0 = posAxis.c2p(pos + bPos - bdPos0, true) + bPosPxOffset;
-        var pos1 = posAxis.c2p(pos + bPos + bdPos1, true) + bPosPxOffset;
-        var posw0 = posAxis.c2p(pos + bPos - wdPos, true) + bPosPxOffset;
-        var posw1 = posAxis.c2p(pos + bPos + wdPos, true) + bPosPxOffset;
-        var posm0 = posAxis.c2p(pos + bPos - bdPos0 * nw, true) + bPosPxOffset;
-        var posm1 = posAxis.c2p(pos + bPos + bdPos1 * nw, true) + bPosPxOffset;
-        var q1 = valAxis.c2p(d.q1, true);
-        var q3 = valAxis.c2p(d.q3, true);
+        var lcenter = posAxis.c2l(d.pos + bPos, true);
+        var posc = posAxis.l2p(lcenter) + bPosPxOffset;
+        var pos0 = posAxis.l2p(lcenter - bdPos0) + bPosPxOffset;
+        var pos1 = posAxis.l2p(lcenter + bdPos1) + bPosPxOffset;
+        var posw0 = posAxis.l2p(lcenter - wdPos) + bPosPxOffset;
+        var posw1 = posAxis.l2p(lcenter + wdPos) + bPosPxOffset;
+        var posm0 = posAxis.l2p(lcenter - bdPos0 * nw) + bPosPxOffset;
+        var posm1 = posAxis.l2p(lcenter + bdPos1 * nw) + bPosPxOffset;
+        var q1 = valAxis.l2p(d.q1, true);
+        var q3 = valAxis.l2p(d.q3, true);
         // make sure median isn't identical to either of the
         // quartiles, so we can see it
         var m = Lib.constrain(
@@ -288,9 +288,10 @@ function plotBoxMean(sel, axes, trace, t) {
     paths.exit().remove();
 
     paths.each(function(d) {
-        var posc = posAxis.c2p(d.pos + bPos, true) + bPosPxOffset;
-        var pos0 = posAxis.c2p(d.pos + bPos - bdPos0, true) + bPosPxOffset;
-        var pos1 = posAxis.c2p(d.pos + bPos + bdPos1, true) + bPosPxOffset;
+        var lcenter = posAxis.c2l(d.pos + bPos, true);
+        var posc = posAxis.l2p(lcenter) + bPosPxOffset;
+        var pos0 = posAxis.l2p(lcenter - bdPos0) + bPosPxOffset;
+        var pos1 = posAxis.l2p(lcenter + bdPos1) + bPosPxOffset;
         var m = valAxis.c2p(d.mean, true);
         var sl = valAxis.c2p(d.mean - d.sd, true);
         var sh = valAxis.c2p(d.mean + d.sd, true);
diff --git a/test/image/baselines/box_log_scale.png b/test/image/baselines/box_log_scale.png
new file mode 100644
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HcmV?d00001

diff --git a/test/image/mocks/box_log_scale.json b/test/image/mocks/box_log_scale.json
new file mode 100644
index 00000000000..e9160f2e346
--- /dev/null
+++ b/test/image/mocks/box_log_scale.json
@@ -0,0 +1,94 @@
+{
+    "data": [
+        {
+            "y": [
+                1.0,
+                1.1,
+                1.0,
+                0.9,
+                1.2,
+                2.0,
+                1.5,
+                2.3,
+                1.7,
+                2.2,
+                1.0,
+                1.1,
+                1.2,
+                0.9,
+                1.1
+            ],
+            "x": [
+                1,
+                1,
+                1,
+                1,
+                1,
+                10,
+                10,
+                10,
+                10,
+                10,
+                100,
+                100,
+                100,
+                100,
+                100
+            ],
+            "type": "box"
+        },
+        {
+            "y": [
+                2.2,
+                2.3,
+                2.0,
+                2.5,
+                2.1,
+                0.1,
+                0.5,
+                0.8,
+                0.3,
+                0.3,
+                1.1,
+                1.2,
+                0.9,
+                1.0,
+                1.0,
+                2.4,
+                2.0,
+                1.5,
+                1.6,
+                1.9
+            ],
+            "x": [
+                1,
+                1,
+                1,
+                1,
+                1,
+                10,
+                10,
+                10,
+                10,
+                10,
+                50,
+                50,
+                50,
+                50,
+                50,
+                100,
+                100,
+                100,
+                100,
+                100
+            ],
+            "type": "box",
+            "boxmean": true
+        }
+    ],
+    "layout": {
+        "xaxis": {
+            "type": "log"
+        }
+    }
+}

From 370e61a25005978d70f716ee38d391dbfa66e21a Mon Sep 17 00:00:00 2001
From: Shumpei Shiina <s417.lama@gmail.com>
Date: Wed, 16 Oct 2019 19:54:30 -0500
Subject: [PATCH 2/5] Don't use linearized values on value axes in box plots

---
 src/traces/box/plot.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/traces/box/plot.js b/src/traces/box/plot.js
index 1f6d3432c66..e6e6bec935e 100644
--- a/src/traces/box/plot.js
+++ b/src/traces/box/plot.js
@@ -94,8 +94,8 @@ function plotBoxAndWhiskers(sel, axes, trace, t) {
         var posw1 = posAxis.l2p(lcenter + wdPos) + bPosPxOffset;
         var posm0 = posAxis.l2p(lcenter - bdPos0 * nw) + bPosPxOffset;
         var posm1 = posAxis.l2p(lcenter + bdPos1 * nw) + bPosPxOffset;
-        var q1 = valAxis.l2p(d.q1, true);
-        var q3 = valAxis.l2p(d.q3, true);
+        var q1 = valAxis.c2p(d.q1, true);
+        var q3 = valAxis.c2p(d.q3, true);
         // make sure median isn't identical to either of the
         // quartiles, so we can see it
         var m = Lib.constrain(

From 1876e8c5caaad78ca7d50fa0282c8e1c780b9d00 Mon Sep 17 00:00:00 2001
From: Shumpei Shiina <s417.lama@gmail.com>
Date: Tue, 22 Oct 2019 10:20:02 -0500
Subject: [PATCH 3/5] remove unnecessary commentout

---
 src/plots/cartesian/autorange.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/plots/cartesian/autorange.js b/src/plots/cartesian/autorange.js
index ca3b16805cb..0843b24666b 100644
--- a/src/plots/cartesian/autorange.js
+++ b/src/plots/cartesian/autorange.js
@@ -385,7 +385,7 @@ function findExtremes(ax, data, opts) {
             // more than an order of mag, clip it to one order. This is so
             // we don't have non-positive errors or absurdly large lower
             // range due to rounding errors
-            // if(isLog && vmin < vmax / 10) vmin = vmax / 10;
+            if(isLog && vmin < vmax / 10) vmin = vmax / 10;
 
             dmin = ax.c2l(vmin);
             dmax = ax.c2l(vmax);

From 1e4aa7e9b0c58bde3466fbe7bb0933f9949f771d Mon Sep 17 00:00:00 2001
From: Shumpei Shiina <s417.lama@gmail.com>
Date: Tue, 22 Oct 2019 10:23:45 -0500
Subject: [PATCH 4/5] restore a deleted new line

---
 src/traces/box/cross_trace_calc.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/traces/box/cross_trace_calc.js b/src/traces/box/cross_trace_calc.js
index b1792cb9794..a56cc156f8a 100644
--- a/src/traces/box/cross_trace_calc.js
+++ b/src/traces/box/cross_trace_calc.js
@@ -125,6 +125,7 @@ function setPositionOffset(traceType, gd, boxList, posAxis) {
         t.bPos = bPos;
         t.bdPos = bdPos;
         t.wHover = wHover;
+
         // box/violin-only value-space push value
         var pushplus;
         var pushminus;

From 349ef640517fc2429e8fb9364f7c30925507fddc Mon Sep 17 00:00:00 2001
From: Shumpei Shiina <s417.lama@gmail.com>
Date: Thu, 24 Oct 2019 20:53:59 -0500
Subject: [PATCH 5/5] Also fix violin traces

---
 src/traces/scatter/line_points.js         |   4 +-
 src/traces/violin/plot.js                 |  11 +--
 test/image/baselines/violin_log_scale.png | Bin 0 -> 25600 bytes
 test/image/mocks/violin_log_scale.json    |  94 ++++++++++++++++++++++
 4 files changed, 102 insertions(+), 7 deletions(-)
 create mode 100644 test/image/baselines/violin_log_scale.png
 create mode 100644 test/image/mocks/violin_log_scale.json

diff --git a/src/traces/scatter/line_points.js b/src/traces/scatter/line_points.js
index 2943f2673bb..89964c92ccd 100644
--- a/src/traces/scatter/line_points.js
+++ b/src/traces/scatter/line_points.js
@@ -67,8 +67,8 @@ module.exports = function linePoints(d, opts) {
     function getPt(index) {
         var di = d[index];
         if(!di) return false;
-        var x = xa.c2p(di.x);
-        var y = ya.c2p(di.y);
+        var x = opts.linearized ? xa.l2p(di.x) : xa.c2p(di.x);
+        var y = opts.linearized ? ya.l2p(di.y) : ya.c2p(di.y);
 
         // if non-positive log values, set them VERY far off-screen
         // so the line looks essentially straight from the previous point.
diff --git a/src/traces/violin/plot.js b/src/traces/violin/plot.js
index a109fd6cab9..f6ca9ac738a 100644
--- a/src/traces/violin/plot.js
+++ b/src/traces/violin/plot.js
@@ -28,7 +28,8 @@ module.exports = function plot(gd, plotinfo, cdViolins, violinLayer) {
             connectGaps: true,
             baseTolerance: 0.75,
             shape: 'spline',
-            simplify: true
+            simplify: true,
+            linearized: true
         });
         return Drawing.smoothopen(segments[0], 1);
     }
@@ -64,8 +65,8 @@ module.exports = function plot(gd, plotinfo, cdViolins, violinLayer) {
             var pathSel = d3.select(this);
             var density = d.density;
             var len = density.length;
-            var posCenter = d.pos + bPos;
-            var posCenterPx = posAxis.c2p(posCenter);
+            var posCenter = posAxis.c2l(d.pos + bPos, true);
+            var posCenterPx = posAxis.l2p(posCenter);
 
             var scale;
             if(trace.width) {
@@ -85,7 +86,7 @@ module.exports = function plot(gd, plotinfo, cdViolins, violinLayer) {
                 for(i = 0; i < len; i++) {
                     pt = pts[i] = {};
                     pt[t.posLetter] = posCenter + (density[i].v / scale);
-                    pt[t.valLetter] = density[i].t;
+                    pt[t.valLetter] = valAxis.c2l(density[i].t, true);
                 }
                 pathPos = makePath(pts);
             }
@@ -95,7 +96,7 @@ module.exports = function plot(gd, plotinfo, cdViolins, violinLayer) {
                 for(k = 0, i = len - 1; k < len; k++, i--) {
                     pt = pts[k] = {};
                     pt[t.posLetter] = posCenter - (density[i].v / scale);
-                    pt[t.valLetter] = density[i].t;
+                    pt[t.valLetter] = valAxis.c2l(density[i].t, true);
                 }
                 pathNeg = makePath(pts);
             }
diff --git a/test/image/baselines/violin_log_scale.png b/test/image/baselines/violin_log_scale.png
new file mode 100644
index 0000000000000000000000000000000000000000..774b9627036b2539af05824555537ec34423a7a0
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diff --git a/test/image/mocks/violin_log_scale.json b/test/image/mocks/violin_log_scale.json
new file mode 100644
index 00000000000..08fc932aa8f
--- /dev/null
+++ b/test/image/mocks/violin_log_scale.json
@@ -0,0 +1,94 @@
+{
+    "data": [
+        {
+            "y": [
+                1.0,
+                1.1,
+                1.0,
+                0.9,
+                1.2,
+                2.0,
+                1.5,
+                2.3,
+                1.7,
+                2.2,
+                1.0,
+                1.1,
+                1.2,
+                0.9,
+                1.1
+            ],
+            "x": [
+                1,
+                1,
+                1,
+                1,
+                1,
+                10,
+                10,
+                10,
+                10,
+                10,
+                100,
+                100,
+                100,
+                100,
+                100
+            ],
+            "type": "violin",
+            "box": {
+                "visible": true
+            },
+            "meanline": {
+                "visible": true
+            },
+            "side": "negative"
+        },
+        {
+            "y": [
+                2.2,
+                2.3,
+                2.0,
+                2.5,
+                2.1,
+                0.1,
+                0.5,
+                0.8,
+                0.3,
+                0.3,
+                2.4,
+                2.0,
+                1.5,
+                1.6,
+                1.9
+            ],
+            "x": [
+                1,
+                1,
+                1,
+                1,
+                1,
+                10,
+                10,
+                10,
+                10,
+                10,
+                100,
+                100,
+                100,
+                100,
+                100
+            ],
+            "type": "violin",
+            "meanline": {
+                "visible": true
+            },
+            "side": "positive"
+        }
+    ],
+    "layout": {
+        "xaxis": {
+            "type": "log"
+        }
+    }
+}