From 9869d24aeba0dde7da534908124dc9096b7595b4 Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Wed, 24 Apr 2024 13:10:41 -0400 Subject: [PATCH 1/9] transferred scripts from separate repo --- python/__pycache__/composite.cpython-39.pyc | Bin 0 -> 2020 bytes python/__pycache__/plot.cpython-39.pyc | Bin 0 -> 8358 bytes .../__pycache__/slidingWindow.cpython-39.pyc | Bin 0 -> 545 bytes python/combined_template.xml | 197 ++++++++++++ python/composite.py | 77 +++++ python/composite_average copy.out | 9 + python/composite_average.out | 9 + python/composite_plot (1).xml | 1 + python/out.xml | 220 +++++++++++++ python/plot.py | 189 +++++++++++ python/plotter.py | 61 ++++ python/sample.out | 3 + python/slidingWindow.py | 9 + python/template.xml | 293 ++++++++++++++++++ 14 files changed, 1068 insertions(+) create mode 100644 python/__pycache__/composite.cpython-39.pyc create mode 100644 python/__pycache__/plot.cpython-39.pyc create mode 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file diff --git a/python/composite.py b/python/composite.py new file mode 100644 index 0000000..d3c4654 --- /dev/null +++ b/python/composite.py @@ -0,0 +1,77 @@ +import numpy as np +import csv +import xml.dom.minidom as dom +import argparse +import math + +class Composite: + def __init__(self, xmin=None, xmax=None, sense=[], anti=[]): + self.xmin = xmin + self.xmax = xmax + self.sense = sense + self.anti = anti + + def __str__(self): + return "Sense: " + str(self.sense) + "\nAnti: " + str(self.anti) + "\nXMin: " + str(self.xmin) + "\nXMax: " + str(self.xmax) + +def parseComposite(file): + fileArr = open(file, "r").read().split("\n") + xmin = None + xmax = None + sense = [] + anti = [] + xmin_curr = 0 + xmax_curr = 0 + offset = 0 + for line in fileArr: + print("line") + # Skip empty + if len(line.strip()) == 0 : + continue + # Separate fields + fields = line.split("\t") + if fields[0] == "" or fields[0] == "NAME": + print("name") + xmin_curr = int(float(fields[1])) + xmax_curr = int(float(fields[-1])) + # If the x domain starts at 0 shift it to the left + if xmin_curr == 0: + xmin_curr -= math.floor(xmax_curr / 2) + xmax_curr -= math.floor(xmax_curr / 2) + # If the x domain is not defined yet, define it + if xmin == None or xmax == None: + xmin = xmin_curr + xmax = xmax_curr + # Redefine min and max if necessary + xmax = max(xmax_curr, xmax) + xmin = min(xmin_curr, xmin) + sense = [0] * (xmax - xmin + 1) + anti = [0] * (xmax - xmin + 1) + + # Add the values to sense and anti arrays + if "sense" in fields[0].lower(): + print("sense") + i = 1 + while i < len(fields): + sense[offset + i - 1] += float(fields[i]) + i += 1 + elif "anti" in fields[0].lower(): + i = 1 + while i < len(fields): + anti[offset + i - 1] += float(fields[i]) + i += 1 + # If the first field is not empty or "NAME" and does not contain "sense" or "anti" parse as combined or midpoint data + elif not (fields[0] == "" or fields[0] == "NAME"): + i = 1 + while i < len(fields): + sense[offset + i - 1] += float(fields[i]) / 2 + anti[offset + i - 1] += float(fields[i]) / 2 + return Composite(xmin, xmax, sense, anti) + + +def main(): + c = parseComposite("sample.out") + print(c) + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/python/composite_average copy.out b/python/composite_average copy.out new file mode 100644 index 0000000..d94dc68 --- /dev/null +++ b/python/composite_average copy.out @@ -0,0 +1,9 @@ + -499.0 -498.0 -497.0 -496.0 -495.0 -494.0 -493.0 -492.0 -491.0 -490.0 -489.0 -488.0 -487.0 -486.0 -485.0 -484.0 -483.0 -482.0 -481.0 -480.0 -479.0 -478.0 -477.0 -476.0 -475.0 -474.0 -473.0 -472.0 -471.0 -470.0 -469.0 -468.0 -467.0 -466.0 -465.0 -464.0 -463.0 -462.0 -461.0 -460.0 -459.0 -458.0 -457.0 -456.0 -455.0 -454.0 -453.0 -452.0 -451.0 -450.0 -449.0 -448.0 -447.0 -446.0 -445.0 -444.0 -443.0 -442.0 -441.0 -440.0 -439.0 -438.0 -437.0 -436.0 -435.0 -434.0 -433.0 -432.0 -431.0 -430.0 -429.0 -428.0 -427.0 -426.0 -425.0 -424.0 -423.0 -422.0 -421.0 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0.3726474278544542 0.335633626097867 0.3594730238393977 0.3657465495608532 0.3670012547051443 0.37829360100376414 0.37327478042659973 0.3582183186951067 0.34880803011292344 0.36511919698870765 0.35257214554579674 0.3713927227101631 0.4096612296110414 + -14.0 -13.0 -12.0 -11.0 -10.0 -9.0 -8.0 -7.0 -6.0 -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 +A_11926_filtered_5read1_sense.cdt 0.3241025641025641 0.30256410256410254 0.28717948717948716 0.3261538461538461 0.32205128205128203 0.3261538461538461 0.3353846153846154 0.31384615384615383 0.32 0.3394871794871795 0.3425641025641026 0.3405128205128205 0.36 0.3230769230769231 0.3343589743589744 0.4194871794871795 0.40102564102564103 0.3712820512820513 0.38256410256410256 0.37025641025641026 0.34564102564102567 0.3128205128205128 0.31794871794871793 0.32 0.32205128205128203 0.3230769230769231 0.3271794871794872 0.3117948717948718 0.3312820512820513 0.35794871794871796 +A_11926_filtered_5read1_anti.cdt 0.3087179487179487 0.3169230769230769 0.3169230769230769 0.32 0.32 0.32 0.30974358974358973 0.3035897435897436 0.32 0.3292307692307692 0.3251282051282051 0.318974358974359 0.2635897435897436 0.24923076923076923 0.3046153846153846 0.358974358974359 0.3569230769230769 0.3415384615384615 0.3353846153846154 0.3241025641025641 0.3128205128205128 0.3076923076923077 0.3302564102564103 0.3364102564102564 0.3169230769230769 0.30153846153846153 0.30974358974358973 0.3230769230769231 0.321025641025641 0.29743589743589743 diff --git a/python/composite_plot (1).xml b/python/composite_plot (1).xml new file mode 100644 index 0000000..549e853 --- /dev/null +++ b/python/composite_plot (1).xml @@ -0,0 +1 @@ +-500500-11Composite plotPosition (bp)Occupancy (AU) \ No newline at end of file diff --git a/python/out.xml b/python/out.xml new file mode 100644 index 0000000..da8eb07 --- /dev/null +++ b/python/out.xml @@ -0,0 +1,220 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Composite plot + Position (bp) + Occupancy (AU) + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/python/plot.py b/python/plot.py new file mode 100644 index 0000000..6bc3c27 --- /dev/null +++ b/python/plot.py @@ -0,0 +1,189 @@ +import numpy as np +import re +import xml.dom.minidom as dom +import argparse +import copy +import slidingWindow + +class Composite: + pass + +class XScale: + def __init__(self, plot): + self.domain = [plot.xmin, plot.xmax, plot.xmax - plot.xmin] + self.range = [plot.margins.get('left'), plot.width - plot.margins.get('right'), plot.width - (plot.margins.get('right') + plot.margins.get('left'))] + self.zero = (plot.width - (plot.margins.get('right') + plot.margins.get('left'))) / 2 + plot.margins.get('left') + + def get(self, value): + return (self.range[2] / self.domain[2]) * value + self.zero + + def inverse(self, value): + return (value - self.zero) * (self.domain[2] / self.range[2]) + +class yScale: + def __init__(self, plot): + self.domain = [plot.ymin, plot.ymax, plot.ymax - plot.ymin] + self.range = [plot.margins.get('top'), plot.height - plot.margins.get('bottom'), plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))] + self.zero = (plot.height - (plot.margins.get('bottom') + plot.margins.get('top'))) / 2 + plot.margins.get('top') if plot.combined is False else self.range[1] + + def get(self, value): + return (self.range[2] / self.domain[2]) * value + self.zero + + def inverse(self, value): + return (value - self.zero) * (self.domain[2] / self.range[2]) + +class Plot: + def __init__(self, title="Composite plot", xmin=-500, xmax=500, ymin=-1, ymax=1, xlabel="Position (bp)", ylabel="Occupancy (AU)", + opacity=1, smoothing=7, bp_shift=0, combined=False, color_trace=False, show_legend=True): + self.title = title + self.xmin = xmin + self.xmax = xmax + self.ymin = ymin + self.ymax = ymax + self.xlabel = xlabel + self.ylabel = ylabel + self.width = 460 + self.height = 300 + self.margins = {'top': 30, 'right': 170, 'bottom': 35, 'left': 40} + self.opacity = opacity + self.smoothing = smoothing + self.bp_shift = bp_shift + self.combined = combined + self.color_trace = color_trace + self.show_legend = show_legend + document = dom.Document() + self.composite_group = document.createElement("g") + self.composite_group.setAttribute("class", "composite plotted") + self.gradients_group = document.createElement("defs") + self.super_group = document.createElement("g") + self.xscale = XScale(self) + self.yscale = yScale(self) + self.num_composites = 0 + + + def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary_color=None, i=None, opacity=None, smoothing=None, bp_shift=None, hide_sense=False, hide_anti=False, baseline=0): + document = dom.Document() + # Set parameters to global values if not specified + opacity = opacity if opacity is not None else self.opacity + smoothing = smoothing if smoothing is not None else self.smoothing + bp_shift = bp_shift if bp_shift is not None else self.bp_shift + if (i is None): + i = self.num_composites + self.num_composites += 1 + else: + i = i + + # Set x domain as array of integers from xmin to xmax + xdomain = [i + xmin for i in range(xmax - xmin + 1)] + if (self.combined): + # Calculate defined x domain after shifting + shifted_xdomain = [x for x in xdomain if x - bp_shift >= xdomain[0] and x - bp_shift <= xdomain[-1] + and x + bp_shift >= xdomain[0] and x + bp_shift <= xdomain[-1]] + shifted_sense = [sense[j] for j in range(len(sense)) if xdomain[j] + bp_shift >= shifted_xdomain[0] + and xdomain[j] + bp_shift <= shifted_xdomain[-1]] + shifted_anti = [anti[j] for j in range(len(anti)) if xdomain[j] + bp_shift >= shifted_xdomain[0] + and xdomain[j] + bp_shift <= shifted_xdomain[-1]] + # Add occupancy for sense and anti + combined_occupancy = [shifted_sense[j] + shifted_anti[j] for j in range(len(shifted_sense))] + # Smooth occupancy with moving average + new_xdomain, smoothed_occupancy = slidingWindow.sliding_window(shifted_xdomain, combined_occupancy, smoothing).values() + # Truncate x domain to x axis limits + truncated_xdomain = [x for x in xdomain if x >= self.xmin and x <= self.xmax] + # Truncate occupancy and scale by scale factor, adding baseline value + scaled_occupancy = [value if (value := d * scale + baseline) > 0 else 0 for j, d in enumerate(smoothed_occupancy) + if int(new_xdomain[j]) >= self.xmin and int(new_xdomain[j]) <= self.xmax] + #Create Composite Trace + document = dom.Document() + if self.color_trace: + white_line = document.createElement("path") + + composite_fill_top = document.createElement("polygon") + composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") + self.composite_group.appendChild(composite_fill_top) + + wide_trace = document.createElement("path") + wide_trace.setAttribute("stroke-width", "1") + wide_trace.setAttribute("stroke", color) + wide_trace.setAttribute("fill", "none") + wide_trace.setAttribute("d", "M" + "L".join(points)) + if not self.color_trace: + wide_trace.setAttribute("stroke", "#FFFFFF") + narrow_trace = copy.deepcopy(wide_trace) + narrow_trace.setAttribute("stroke-width", "0.5") + narrow_trace.setAttribute("stroke", "#000000") + narrow_trace.setAttribute("d", "M" + "L".join(points)) + self.composite_group.appendChild(wide_trace) + self.composite_group.appendChild(narrow_trace) + else: + # Smooth sense and anti occupancy with moving average + new_xdomain, smoothed_sense = slidingWindow.sliding_window(xdomain, sense, smoothing).values() + smoothed_anti = list(slidingWindow.sliding_window(xdomain, anti, smoothing).values())[1] + # Truncate x domain to x axis limits + truncated_sense_domain = [j for x in new_xdomain if (j := x + bp_shift) >= self.xmin and j <= self.xmax] + truncated_anti_domain = [j for x in new_xdomain if (j := x - bp_shift) >= self.xmin and j <= self.xmax] + # Truncate sense and anti occupancy and scale by scale factor + scaled_sense = [value if (value := d * scale + baseline) > 0 else 0 for j, d in enumerate(smoothed_sense) + if int(new_xdomain[j] + bp_shift) >= self.xmin and int(new_xdomain[j] + bp_shift) <= self.xmax] + scaled_anti = [value if (value := d * scale + baseline) > 0 else 0 for j, d in enumerate(smoothed_anti) + if int(new_xdomain[j] - bp_shift) >= self.xmin and int(new_xdomain[j] - bp_shift) <= self.xmax] + # Create sense path and gradient if not hidden + # Create top polygon + composite_fill_top = document.createElement("polygon") + composite_fill_top.setAttribute("points", pointsA := " ".join([f"{self.xscale.get(d)},{self.yscale.get(-scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") + # Create bottom polygon + composite_fill_bottom = document.createElement("polygon") + composite_fill_bottom.setAttribute("points", pointsB := " ".join([f"{self.xscale.get(d)},{self.yscale.get(scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") + composite_fill_bottom.setAttribute("fill", "url(#composite-gradient-bottom" + str(i) + ")") + + self.composite_group.appendChild(composite_fill_top) + self.composite_group.appendChild(composite_fill_bottom) + self.generateGradients(1, i, color, secondary_color=secondary_color) + self.super_group.appendChild(self.gradients_group) + self.super_group.appendChild(self.composite_group) + return self.super_group + + def generateGradients(self, opacity, i, color, secondary_color=None): + # Creates DOM elements for top and bottom gradients + secondary_color = secondary_color if secondary_color is not None else color + + document = dom.Document() + composite_gradient_top = document.createElement("linearGradient") + composite_gradient_top.setAttribute("class", "composite-gradient-top") + composite_gradient_top.setAttribute("x1", "0%") + composite_gradient_top.setAttribute("x2", "0%") + composite_gradient_top.setAttribute("y1", "0%") + composite_gradient_top.setAttribute("y2", "100%") + composite_gradient_top.setAttribute("id", "composite-gradient-top" + str(i)) + top_stop_one = document.createElement("stop") + top_stop_one.setAttribute("offset", "0") + top_stop_one.setAttribute("stop-color", color) + top_stop_one.setAttribute("stop-opacity", str(opacity)) + top_stop_two = document.createElement("stop") + top_stop_two.setAttribute("offset", "1") + top_stop_two.setAttribute("stop-color", color) + top_stop_two.setAttribute("stop-opacity", "0") + composite_gradient_top.appendChild(top_stop_one) + composite_gradient_top.appendChild(top_stop_two) + self.gradients_group.appendChild(composite_gradient_top) + + composite_gradient_bottom = document.createElement("linearGradient") + composite_gradient_bottom.setAttribute("class", "composite-gradient-bottom") + composite_gradient_bottom.setAttribute("x1", "0%") + composite_gradient_bottom.setAttribute("x2", "0%") + composite_gradient_bottom.setAttribute("y1", "100%") + composite_gradient_bottom.setAttribute("y2", "0%") + composite_gradient_bottom.setAttribute("id", "composite-gradient-bottom" + str(i)) + bottom_stop_one = document.createElement("stop") + bottom_stop_one.setAttribute("offset", "0") + bottom_stop_one.setAttribute("stop-color", secondary_color) + bottom_stop_one.setAttribute("stop-opacity", str(opacity)) + bottom_stop_two = document.createElement("stop") + bottom_stop_two.setAttribute("offset", "1") + bottom_stop_two.setAttribute("stop-color", secondary_color) + bottom_stop_two.setAttribute("stop-opacity", "0") + composite_gradient_bottom.appendChild(bottom_stop_one) + composite_gradient_bottom.appendChild(bottom_stop_two) + + self.gradients_group.appendChild(composite_gradient_bottom) diff --git a/python/plotter.py b/python/plotter.py new file mode 100644 index 0000000..79f6d39 --- /dev/null +++ b/python/plotter.py @@ -0,0 +1,61 @@ +import numpy as np +import plot +import composite +import re +import xml.dom.minidom as dom +import argparse + +def generateSVG(plot): + document = dom.Document() + group = document.appendChild(document.createElement('g')) + title = document.createElement('text') + title.setAttribute("font-size", "16") + title.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) + title.setAttribute("y", "20") + title.setAttribute("label", "title") + title.setAttribute("id", "main-plot-title") + title.setAttribute("style", "text-anchor: middle; cursor: pointer;") + title.appendChild(document.createTextNode(plot.title)) + + xlabel = document.createElement('text') + xlabel.setAttribute("font-size", "16") + xlabel.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) + xlabel.setAttribute("y", str(plot.height - 5)) + xlabel.setAttribute("label", "xlabel") + xlabel.setAttribute("id", "main-plot-xlabel") + xlabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") + xlabel.appendChild(document.createTextNode(plot.xlabel)) + + ylabel = document.createElement('text') + ylabel.setAttribute("font-size", "16") + ylabel.setAttribute("x", "12") + ylabel.setAttribute("y", str((plot.height + plot.margins.get('top') - plot.margins.get('bottom')) / 2)) + ylabel.setAttribute("label", "ylabel") + ylabel.setAttribute("id", "main-plot-ylabel") + ylabel.setAttribute("transform", "rotate(-90 12 147.5)") + ylabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") + ylabel.appendChild(document.createTextNode(plot.ylabel)) + + composite_group = document.createElement('g') + legend = document.createElement('g') + legend.setAttribute("transform", "translate(" + str(plot.width - plot.margins.get("right") + 25) + " " + str(plot.margins.get("top")) + ")") + + group.appendChild(title) + group.appendChild(xlabel) + group.appendChild(ylabel) + + c = composite.parseComposite("sample.out") + group.appendChild(plot.plot_composite(c.xmin, c.xmax, c.sense, c.anti, scale=30, color="#FF0000", secondary_color="#0000FF")) + + template = open("combined_template.xml", "r").read() + with open("out.xml", 'w') as f: + f.write(template + "\n\t") + group.writexml(f, addindent=' ', newl='\n') + f.write("") + +def main(): + p = plot.Plot(combined=True) + generateSVG(p) + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/python/sample.out b/python/sample.out new file mode 100644 index 0000000..e5c6a33 --- /dev/null +++ b/python/sample.out @@ -0,0 +1,3 @@ +NAME 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 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0.0265683141752575 0.0251061235824741 0.025666111469072 0.02924381185567 0.0262572097938143 0.0260083262886596 0.0255416697164947 0.0312348798969071 0.0265683141752576 0.0289949283505153 0.0282793882731957 diff --git a/python/slidingWindow.py b/python/slidingWindow.py new file mode 100644 index 0000000..023c5fa --- /dev/null +++ b/python/slidingWindow.py @@ -0,0 +1,9 @@ +def sliding_window(x_domain, occupancy, window): + occupancy_val = sum(occupancy[:window]) / window + new_xdomain = [(x_domain[0] + x_domain[window - 1]) / 2] + new_occupancy = [occupancy_val] + for i in range(len(occupancy) - window - 1): + new_xdomain.append((x_domain[i + 1] + x_domain[i + window]) / 2) # Added parentheses here + occupancy_val += (occupancy[i + window] - occupancy[i]) / window + new_occupancy.append(occupancy_val) + return {"new_xdomain": new_xdomain, "new_occupancy": new_occupancy} \ No newline at end of file diff --git a/python/template.xml b/python/template.xml new file mode 100644 index 0000000..f229197 --- /dev/null +++ b/python/template.xml @@ -0,0 +1,293 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From dfae17389ce6d56593e83cb71324c2da32f25360 Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Tue, 30 Apr 2024 23:40:09 -0400 Subject: [PATCH 2/9] added very basic argument parsing tick marks are next --- .gitignore | 5 + python/__pycache__/composite.cpython-39.pyc | Bin 2020 -> 3464 bytes python/__pycache__/plot.cpython-39.pyc | Bin 8358 -> 8828 bytes python/combined_template.xml | 197 ------------- python/composite.py | 127 +++++---- python/composite_average copy.out | 9 - python/composite_average.out | 9 - python/composite_plot (1).xml | 1 - python/out.xml | 115 +++++++- python/plot.py | 72 +++-- python/plotter.py | 80 +++++- python/sample.out | 3 - python/template.xml | 293 -------------------- 13 files changed, 302 insertions(+), 609 deletions(-) delete mode 100644 python/combined_template.xml delete mode 100644 python/composite_average copy.out delete mode 100644 python/composite_average.out delete mode 100644 python/composite_plot (1).xml delete mode 100644 python/sample.out delete mode 100644 python/template.xml diff --git a/.gitignore b/.gitignore index 79b5594..3e89745 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,6 @@ +js/* +* **/.DS_Store + +!.gitignore +!python \ No newline at end of file diff --git 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Composite: - def __init__(self, xmin=None, xmax=None, sense=[], anti=[]): + def __init__(self, xmin=None, xmax=None, sense=[], anti=[], id=""): self.xmin = xmin self.xmax = xmax self.sense = sense self.anti = anti + self.id = id def __str__(self): - return "Sense: " + str(self.sense) + "\nAnti: " + str(self.anti) + "\nXMin: " + str(self.xmin) + "\nXMax: " + str(self.xmax) + return "Sense: " + str(self.sense) + "\nAnti: " + str(self.anti) + "\nXMin: " + str(self.xmin) + "\nXMax: " + str(self.xmax) + "\nID:" + str(self.id) -def parseComposite(file): - fileArr = open(file, "r").read().split("\n") - xmin = None - xmax = None - sense = [] - anti = [] - xmin_curr = 0 - xmax_curr = 0 - offset = 0 - for line in fileArr: - print("line") - # Skip empty - if len(line.strip()) == 0 : - continue - # Separate fields - fields = line.split("\t") - if fields[0] == "" or fields[0] == "NAME": - print("name") - xmin_curr = int(float(fields[1])) - xmax_curr = int(float(fields[-1])) - # If the x domain starts at 0 shift it to the left - if xmin_curr == 0: - xmin_curr -= math.floor(xmax_curr / 2) - xmax_curr -= math.floor(xmax_curr / 2) - # If the x domain is not defined yet, define it - if xmin == None or xmax == None: - xmin = xmin_curr - xmax = xmax_curr - # Redefine min and max if necessary - xmax = max(xmax_curr, xmax) - xmin = min(xmin_curr, xmin) - sense = [0] * (xmax - xmin + 1) - anti = [0] * (xmax - xmin + 1) +class CompositeGroup: + def __init__(self): + self.xmin = 0 + self.xmax = 0 + self.sense = [] + self.anti = [] + self.individual_composites = {} + self.files_loaded = len(self.individual_composites) + + def loadComposite(self,composite: Composite): + # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain + self.xmin = min(composite.xmin, self.xmin) + self.xmax = max(composite.xmax, self.xmax) + if len(self.individual_composites) == 0: + self.sense = [0] * (composite.xmax - composite.xmin + 1) + self.anti = [0] * (composite.xmax - composite.xmin + 1) + else: + xmin = min([int(self.individual_composites[c].xmin) for c in self.individual_composites]) + xmax = max([int(self.individual_composites[c].xmax) for c in self.individual_composites]) + prefix = [0] * (xmin - self.xmin) + suffix = [0] * (self.xmax - xmax) + self.sense = prefix + self.sense + suffix + self.anti = prefix + self.anti + suffix + + # Update sense and anti arrays + j = composite.xmin - self.xmin + while j <= composite.xmax - composite.xmin: + idx = composite.xmin - self.xmin + j + self.sense[idx] += composite.sense[j] + self.anti[idx] += composite.anti[j] + j += 1 + + self.individual_composites[composite.id] = composite + + def loadCompositeDict(self,compositeDict: dict): + for composite in compositeDict: + # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain + self.xmin = min(composite.xmin, self.xmin) + self.xmax = max(composite.xmax, self.xmax) + if len(self.individual_composites) == 0: + self.sense = [0] * (composite.xmax - composite.xmin + 1) + self.anti = [0] * (composite.xmax - composite.xmin + 1) + else: + xmin = min([c.xmin for c in self.individual_composites]) + xmax = max([c.xmax for c in self.individual_composites]) + prefix = [0] * (xmin - self.xmin) + suffix = [0] * (self.xmax - xmax) + self.sense = prefix + self.sense + suffix + self.anti = prefix + self.anti + suffix - # Add the values to sense and anti arrays - if "sense" in fields[0].lower(): - print("sense") - i = 1 - while i < len(fields): - sense[offset + i - 1] += float(fields[i]) - i += 1 - elif "anti" in fields[0].lower(): - i = 1 - while i < len(fields): - anti[offset + i - 1] += float(fields[i]) - i += 1 - # If the first field is not empty or "NAME" and does not contain "sense" or "anti" parse as combined or midpoint data - elif not (fields[0] == "" or fields[0] == "NAME"): - i = 1 - while i < len(fields): - sense[offset + i - 1] += float(fields[i]) / 2 - anti[offset + i - 1] += float(fields[i]) / 2 - return Composite(xmin, xmax, sense, anti) + # Update sense and anti arrays + j = composite.xmin - self.xmin + while j <= composite.xmax - composite.xmin: + idx = composite.xmin - self.xmin + j + self.sense[idx] += composite.sense[j] + self.anti[idx] += composite.anti[j] + j += 1 + self.individual_composites[composite.id] = composite + + def __str__(self): + return str(self.individual_composites) def main(): - c = parseComposite("sample.out") - print(c) + c = parseComposite.parseComposite("sample_composites/sample_1.out") + compositeGroup = CompositeGroup() + compositeGroup.loadComposite(c) + c2 = parseComposite.parseComposite("sample_composites/sample2.out.txt") + compositeGroup.loadComposite(c2) + print(compositeGroup) + if __name__ == "__main__": main() \ No newline at end of file diff --git a/python/composite_average copy.out b/python/composite_average copy.out deleted file mode 100644 index d94dc68..0000000 --- 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0.3241025641025641 0.30256410256410254 0.28717948717948716 0.3261538461538461 0.32205128205128203 0.3261538461538461 0.3353846153846154 0.31384615384615383 0.32 0.3394871794871795 0.3425641025641026 0.3405128205128205 0.36 0.3230769230769231 0.3343589743589744 0.4194871794871795 0.40102564102564103 0.3712820512820513 0.38256410256410256 0.37025641025641026 0.34564102564102567 0.3128205128205128 0.31794871794871793 0.32 0.32205128205128203 0.3230769230769231 0.3271794871794872 0.3117948717948718 0.3312820512820513 0.35794871794871796 -A_11926_filtered_5read1_anti.cdt 0.3087179487179487 0.3169230769230769 0.3169230769230769 0.32 0.32 0.32 0.30974358974358973 0.3035897435897436 0.32 0.3292307692307692 0.3251282051282051 0.318974358974359 0.2635897435897436 0.24923076923076923 0.3046153846153846 0.358974358974359 0.3569230769230769 0.3415384615384615 0.3353846153846154 0.3241025641025641 0.3128205128205128 0.3076923076923077 0.3302564102564103 0.3364102564102564 0.3169230769230769 0.30153846153846153 0.30974358974358973 0.3230769230769231 0.321025641025641 0.29743589743589743 diff --git a/python/composite_plot (1).xml b/python/composite_plot (1).xml deleted file mode 100644 index 549e853..0000000 --- a/python/composite_plot (1).xml +++ /dev/null @@ -1 +0,0 @@ --500500-11Composite plotPosition (bp)Occupancy (AU) \ No newline at end of file diff --git a/python/out.xml b/python/out.xml index da8eb07..75649fb 100644 --- a/python/out.xml +++ b/python/out.xml @@ -193,12 +193,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Composite plot - Position (bp) - Occupancy (AU) @@ -211,10 +304,20 @@ - - - + + + + + + + Composite plot + Position (bp) + Occupancy (AU) + -500 + 500 + -1 + 1 \ No newline at end of file diff --git a/python/plot.py b/python/plot.py index 6bc3c27..03ec593 100644 --- a/python/plot.py +++ b/python/plot.py @@ -12,7 +12,7 @@ class XScale: def __init__(self, plot): self.domain = [plot.xmin, plot.xmax, plot.xmax - plot.xmin] self.range = [plot.margins.get('left'), plot.width - plot.margins.get('right'), plot.width - (plot.margins.get('right') + plot.margins.get('left'))] - self.zero = (plot.width - (plot.margins.get('right') + plot.margins.get('left'))) / 2 + plot.margins.get('left') + self.zero = (plot.width - (plot.margins.get('right') + plot.margins.get('left'))) * (abs(plot.xmin) / (abs(plot.xmin) + abs(plot.xmax))) + plot.margins.get('left') def get(self, value): return (self.range[2] / self.domain[2]) * value + self.zero @@ -72,7 +72,6 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary self.num_composites += 1 else: i = i - # Set x domain as array of integers from xmin to xmax xdomain = [i + xmin for i in range(xmax - xmin + 1)] if (self.combined): @@ -88,33 +87,28 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary # Smooth occupancy with moving average new_xdomain, smoothed_occupancy = slidingWindow.sliding_window(shifted_xdomain, combined_occupancy, smoothing).values() # Truncate x domain to x axis limits - truncated_xdomain = [x for x in xdomain if x >= self.xmin and x <= self.xmax] + truncated_xdomain = [x for x in new_xdomain if x >= self.xmin and x <= self.xmax] # Truncate occupancy and scale by scale factor, adding baseline value scaled_occupancy = [value if (value := d * scale + baseline) > 0 else 0 for j, d in enumerate(smoothed_occupancy) if int(new_xdomain[j]) >= self.xmin and int(new_xdomain[j]) <= self.xmax] - #Create Composite Trace - document = dom.Document() - if self.color_trace: - white_line = document.createElement("path") - composite_fill_top = document.createElement("polygon") composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") self.composite_group.appendChild(composite_fill_top) - + #Create outline wide_trace = document.createElement("path") wide_trace.setAttribute("stroke-width", "1") wide_trace.setAttribute("stroke", color) wide_trace.setAttribute("fill", "none") wide_trace.setAttribute("d", "M" + "L".join(points)) + self.composite_group.appendChild(wide_trace) if not self.color_trace: wide_trace.setAttribute("stroke", "#FFFFFF") narrow_trace = copy.deepcopy(wide_trace) narrow_trace.setAttribute("stroke-width", "0.5") narrow_trace.setAttribute("stroke", "#000000") narrow_trace.setAttribute("d", "M" + "L".join(points)) - self.composite_group.appendChild(wide_trace) - self.composite_group.appendChild(narrow_trace) + self.composite_group.appendChild(narrow_trace) else: # Smooth sense and anti occupancy with moving average new_xdomain, smoothed_sense = slidingWindow.sliding_window(xdomain, sense, smoothing).values() @@ -127,19 +121,49 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary if int(new_xdomain[j] + bp_shift) >= self.xmin and int(new_xdomain[j] + bp_shift) <= self.xmax] scaled_anti = [value if (value := d * scale + baseline) > 0 else 0 for j, d in enumerate(smoothed_anti) if int(new_xdomain[j] - bp_shift) >= self.xmin and int(new_xdomain[j] - bp_shift) <= self.xmax] - # Create sense path and gradient if not hidden - # Create top polygon - composite_fill_top = document.createElement("polygon") - composite_fill_top.setAttribute("points", pointsA := " ".join([f"{self.xscale.get(d)},{self.yscale.get(-scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") - composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") - # Create bottom polygon - composite_fill_bottom = document.createElement("polygon") - composite_fill_bottom.setAttribute("points", pointsB := " ".join([f"{self.xscale.get(d)},{self.yscale.get(scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") - composite_fill_bottom.setAttribute("fill", "url(#composite-gradient-bottom" + str(i) + ")") - - self.composite_group.appendChild(composite_fill_top) - self.composite_group.appendChild(composite_fill_bottom) - self.generateGradients(1, i, color, secondary_color=secondary_color) + # Create sense trace and polygon if not hidden + if not hide_anti: + # Create top polygon + composite_fill_top = document.createElement("polygon") + composite_fill_top.setAttribute("points", " ".join(sense_points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") + self.composite_group.appendChild(composite_fill_top) + #Create trace + top_wide_trace = document.createElement("path") + top_wide_trace.setAttribute("stroke-width", "1") + top_wide_trace.setAttribute("stroke", color) + top_wide_trace.setAttribute("fill", "none") + top_wide_trace.setAttribute("d", "M" + "L".join(sense_points)) + self.composite_group.appendChild(top_wide_trace) + if not self.color_trace: + top_wide_trace.setAttribute("stroke", "#FFFFFF") + top_narrow_trace = copy.deepcopy(top_wide_trace) + top_narrow_trace.setAttribute("stroke-width", "0.5") + top_narrow_trace.setAttribute("stroke", "#000000") + top_narrow_trace.setAttribute("d", "M" + "L".join(sense_points)) + self.composite_group.appendChild(top_narrow_trace) + # Create anti trace and polygon if not hidden + if not hide_anti: + # Create polygon + composite_fill_bottom = document.createElement("polygon") + composite_fill_bottom.setAttribute("points", " ".join(anti_points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") + composite_fill_bottom.setAttribute("fill", "url(#composite-gradient-bottom" + str(i) + ")") + self.composite_group.appendChild(composite_fill_bottom) + #Create trace + bottom_wide_trace = document.createElement("path") + bottom_wide_trace.setAttribute("stroke-width", "1") + bottom_wide_trace.setAttribute("stroke", secondary_color) + bottom_wide_trace.setAttribute("fill", "none") + bottom_wide_trace.setAttribute("d", "M" + "L".join(anti_points)) + self.composite_group.appendChild(bottom_wide_trace) + if not self.color_trace: + bottom_wide_trace.setAttribute("stroke", "#FFFFFF") + bottom_narrow_trace = copy.deepcopy(bottom_wide_trace) + bottom_narrow_trace.setAttribute("stroke-width", "0.5") + bottom_narrow_trace.setAttribute("stroke", "#000000") + bottom_narrow_trace.setAttribute("d", "M" + "L".join(anti_points)) + self.composite_group.appendChild(bottom_narrow_trace) + self.generateGradients(opacity, i, color, secondary_color=secondary_color) self.super_group.appendChild(self.gradients_group) self.super_group.appendChild(self.composite_group) return self.super_group diff --git a/python/plotter.py b/python/plotter.py index 79f6d39..7098d0b 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -4,10 +4,12 @@ import re import xml.dom.minidom as dom import argparse +import parseComposite + +document = dom.Document() +group = document.appendChild(document.createElement('g')) def generateSVG(plot): - document = dom.Document() - group = document.appendChild(document.createElement('g')) title = document.createElement('text') title.setAttribute("font-size", "16") title.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) @@ -37,25 +39,81 @@ def generateSVG(plot): ylabel.appendChild(document.createTextNode(plot.ylabel)) composite_group = document.createElement('g') + legend = document.createElement('g') legend.setAttribute("transform", "translate(" + str(plot.width - plot.margins.get("right") + 25) + " " + str(plot.margins.get("top")) + ")") + xmin = document.createElement('text') + xmin.setAttribute("x", str(plot.margins.get("left"))) + xmin.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) + xmin.setAttribute("text-anchor", "middle") + xmin.setAttribute("font-size", "14px") + xmin.appendChild(document.createTextNode(str(plot.xmin))) + + xmax = document.createElement('text') + xmax.setAttribute("x", str(plot.width - plot.margins.get("right"))) + xmax.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) + xmax.setAttribute("text-anchor", "middle") + xmax.setAttribute("font-size", "14px") + xmax.appendChild(document.createTextNode(str(plot.xmax))) + + ymin = document.createElement('text') + ymin.setAttribute("x", "30") + ymin.setAttribute("y", str(plot.height - plot.margins.get("bottom"))) + ymin.setAttribute("text-anchor", "middle") + ymin.setAttribute("font-size", "14px") + ymin.appendChild(document.createTextNode(str(plot.ymin))) + + ymax = document.createElement('text') + ymax.setAttribute("x", "30") + ymax.setAttribute("y", str(plot.margins.get("top") + 10)) + ymax.setAttribute("text-anchor", "middle") + ymax.setAttribute("font-size", "14px") + ymax.appendChild(document.createTextNode(str(plot.ymax))) + + group.appendChild(title) group.appendChild(xlabel) group.appendChild(ylabel) + group.appendChild(xmin) + group.appendChild(xmax) + group.appendChild(ymin) + group.appendChild(ymax) + +def main(): + return True - c = composite.parseComposite("sample.out") - group.appendChild(plot.plot_composite(c.xmin, c.xmax, c.sense, c.anti, scale=30, color="#FF0000", secondary_color="#0000FF")) - template = open("combined_template.xml", "r").read() + +if __name__ == "__main__": + p = plot.Plot(combined=False, color_trace=False, opacity=1, xmin=-500) + + parser = argparse.ArgumentParser() + parser.add_argument("composites", nargs="+") + args = parser.parse_args() + for g in args.composites: + composite_group = composite.CompositeGroup() + composite_files = g.split("-") + for c in composite_files: + #Check if composite file contains multiple composites + if sum(1 for line in open(c) if len(line.strip()) != 0) <= 3: + composite = parseComposite.parseComposite(c) + composite_group.loadComposite(composite) + else: + prefixes = parseComposite.get_prefixes_from_multiple_composites(c) + composites = parseComposite.parse_multiple_composite(c, prefixes) + composite_group.loadCompositeDict(composites) + group.appendChild(p.plot_composite(composite_group.xmin, composite_group.xmax, composite_group.sense, composite_group.anti, scale=15, color="#FF0000", secondary_color="#0000FF")) + + generateSVG(p) + if p.combined: + template = open("resources/combined_template.xml", "r").read() + else: + template = open("resources/template.xml", "r").read() with open("out.xml", 'w') as f: f.write(template + "\n\t") group.writexml(f, addindent=' ', newl='\n') f.write("") -def main(): - p = plot.Plot(combined=True) - generateSVG(p) - -if __name__ == "__main__": - main() \ No newline at end of file + + print(args.composites) diff --git a/python/sample.out b/python/sample.out deleted file mode 100644 index e5c6a33..0000000 --- a/python/sample.out +++ /dev/null @@ -1,3 +0,0 @@ -NAME 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From 74fc3f698de172cfe899510aa2410c2d2b0e588d Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Wed, 8 May 2024 19:30:19 -0400 Subject: [PATCH 3/9] save before parsing is added --- js/events/load_composite_button.js | 1 + js/parse_composite.js | 4 +- js/widgets/main_plot.js | 16 +- python/__pycache__/plot.cpython-39.pyc | Bin 8828 -> 8838 bytes python/composite.py | 12 +- python/out.xml | 443 ++++++++----------------- python/plot.py | 148 ++++++++- python/plotter.py | 257 ++++++++++++-- 8 files changed, 522 insertions(+), 359 deletions(-) diff --git a/js/events/load_composite_button.js b/js/events/load_composite_button.js index 85b0e25..c9dd1a4 100644 --- a/js/events/load_composite_button.js +++ b/js/events/load_composite_button.js @@ -19,6 +19,7 @@ $(function() { $("#metadata-table").metadata_table("add_row", [id]); $("#settings-table").settings_table("add_row", [id]); }; + console.log(prefixes) $("#settings-table").settings_table("plot_all_composites", {xmin: xmin, xmax: xmax, ymax: ymax}, allow_shrink=true); $("#main-plot").main_plot("update_legend") diff --git a/js/parse_composite.js b/js/parse_composite.js index 11fb78b..fbba6fd 100644 --- a/js/parse_composite.js +++ b/js/parse_composite.js @@ -129,6 +129,7 @@ let parse_multiple_composite = function(text, prefix) { if (col0 === "" || col0 === "NAME") { // If the x domain is defined, save the composite if (save_comp) { + console.log(id) composites[id] = {xmin: xmin, xmax: xmax, sense: sense, anti: anti} }; save_comp = false; @@ -142,6 +143,7 @@ let parse_multiple_composite = function(text, prefix) { } } else if (col0.startsWith(prefix)){ id = col0.slice(prefix.length).split("_")[0]; + console.log(id) save_comp = true; if (col0.toLowerCase().includes("sense")) { sense = fields.slice(1).map(parseFloat) @@ -160,6 +162,6 @@ let parse_multiple_composite = function(text, prefix) { if (save_comp) { composites[id] = {xmin: xmin, xmax: xmax, sense: sense, anti: anti} }; - + console.log(composites) return composites } \ No newline at end of file diff --git a/js/widgets/main_plot.js b/js/widgets/main_plot.js index bad2615..e15c5e4 100644 --- a/js/widgets/main_plot.js +++ b/js/widgets/main_plot.js @@ -171,8 +171,8 @@ $(function() { d3.select("#main-plot-div").on("mousemove", function(e) { $("#main-plot").main_plot("move_tooltip", e) }); - main_plot.on("mouseleave", function() { - // $("#main-plot").main_plot("hide_tooltip") + d3.select("#main-plot-div").on("mouseleave", function() { + $("#main-plot").main_plot("hide_tooltip") }); this.enable_tooltip = true; @@ -315,6 +315,8 @@ $(function() { plot_composite: function(xmin, xmax, sense, anti, scale, color, secondary_color, i, opacity, smoothing, bp_shift, hide, hide_sense=false, hide_anti=false, baseline=0) { // Set composite visibility + console.log("xmin:" + xmin) + console.log("xmax:" + xmax) let composite = this._elements.composites[i] .classed("plotted", !hide) .style("display", hide ? "none" : null), @@ -345,6 +347,7 @@ $(function() { scaled_occupancy = smoothed_occupancy.filter((_, j) => new_xdomain[j] >= this.xmin && new_xdomain[j] <= this.xmax) .map(d => ((value = d * scale + baseline) > 0)? value: 0); + console.log(truncated_xdomain) // Set fill color composite.select(".composite-gradient-top") .selectAll("stop") @@ -737,8 +740,10 @@ $(function() { if (color_trace) { this._elements.composite_group.selectAll(".composite .color-line-top") .style("display", null); - this._elements.composite_group.selectAll(".composite .color-line-bottom") - .style("display", null); + if (!this.combined){ + this._elements.composite_group.selectAll(".composite .color-line-bottom") + .style("display", null); + } this._elements.composite_group.selectAll(".composite .white-line") .style("display", "none"); this._elements.composite_group.selectAll(".composite .black-line") @@ -820,12 +825,13 @@ $(function() { .style("left", ev.clientX - (w - 80) / 1.4) } else { this._elements.tooltip.style("display", "none") + d3.selectAll("#composite-plot-tooltip").remove(); } } }, hide_tooltip: function() { - this._elements.tooltip.style("display", "none") + d3.selectAll("#composite-plot-tooltip").remove(); }, download_as_svg: function() { diff --git a/python/__pycache__/plot.cpython-39.pyc b/python/__pycache__/plot.cpython-39.pyc index a1201b23b246c3bfdc5ff4a1610198cb6af811c9..25c38d6dd5c7bd24a95ed901c8fea0c565acf49a 100644 GIT binary patch delta 1448 zcmZXTOH7kN5XZZHe9%G#rKJxnrA4V#&|nnA0$N@^(1_M&QL(fip*+5?Zc&TT=t-~Y z#FHd?_7rSu{x>wicI4JBV;WI2t`CPY~9j1`W zEe*+%A?^v#IhU@WE`F5WxLRu)Aj%i~lgAo&FC}~(-bMD4wJuut032$7L12^?+z}Tp z8-qFw$d;w)y?e0MQ1WwJpH`DrP1jU@mRjp`+fKphuz)yDw*M$L+`vCK3-uDVkbk1N z9K&Z<`&};i#XVPhPeVKdj0!9&{2XL?%XvsLOL^7*l?rQt9(n^*@0|#)Jcers{U&9B9g{<533>)9uiH7NOT6kKmV33+thp@D?Qqw+QVGcmD?AFDI!0 delta 1366 zcmZvcNla5w6o$F9JW5MLp*-8tDzB|l3ZlUvQ>CB`qEy4=R8e?Bi43;&f{G?4>Owch zgq*l>Txo(aQN!AWE0?a^Jfn#lG*&`-4M|(_nn3q17`q&0~;dfK7`3Zez4l2y~Nvf$bpSy*CmjGVsQPRr# 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smoothing=None, bp_shift=None, hide_sense=False, hide_anti=False, baseline=0, name=None): self.xmin = 0 self.xmax = 0 self.sense = [] self.anti = [] + self.scale = scale + self.color = color + self.secondary_color = secondary_color if secondary_color is not None else color + self.opacity = opacity + self.smoothing = smoothing + self.bp_shift = bp_shift + self.hide_anti = hide_anti + self.baseline = baseline + self.hide_sense = hide_sense self.individual_composites = {} self.files_loaded = len(self.individual_composites) + self.name = name def loadComposite(self,composite: Composite): # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain diff --git a/python/out.xml b/python/out.xml index 75649fb..6a0fbb2 100644 --- a/python/out.xml +++ b/python/out.xml @@ -1,323 +1,146 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + -0.6 + + + + + + composite_one + + + + + + composite_two + + + + + + composite_three + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Composite plot Position (bp) - Occupancy (AU) - -500 - 500 - -1 - 1 - - \ No newline at end of file + + Occupancy (AU) X10 + -1 + + -549 + 550 + 0.6 + diff --git a/python/plot.py b/python/plot.py index 03ec593..e7863ac 100644 --- a/python/plot.py +++ b/python/plot.py @@ -4,12 +4,14 @@ import argparse import copy import slidingWindow +import math class Composite: pass class XScale: def __init__(self, plot): + self.plot = plot self.domain = [plot.xmin, plot.xmax, plot.xmax - plot.xmin] self.range = [plot.margins.get('left'), plot.width - plot.margins.get('right'), plot.width - (plot.margins.get('right') + plot.margins.get('left'))] self.zero = (plot.width - (plot.margins.get('right') + plot.margins.get('left'))) * (abs(plot.xmin) / (abs(plot.xmin) + abs(plot.xmax))) + plot.margins.get('left') @@ -22,12 +24,12 @@ def inverse(self, value): class yScale: def __init__(self, plot): - self.domain = [plot.ymin, plot.ymax, plot.ymax - plot.ymin] + self.domain = [plot.ymin, plot.ymax, abs(plot.ymax) + abs(plot.ymin)] self.range = [plot.margins.get('top'), plot.height - plot.margins.get('bottom'), plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))] - self.zero = (plot.height - (plot.margins.get('bottom') + plot.margins.get('top'))) / 2 + plot.margins.get('top') if plot.combined is False else self.range[1] + self.zero = (plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))) * (0.5) + plot.margins.get('top') if plot.combined is False else self.range[1] def get(self, value): - return (self.range[2] / self.domain[2]) * value + self.zero + return self.zero - (self.range[2] / self.domain[2]) * value def inverse(self, value): return (value - self.zero) * (self.domain[2] / self.range[2]) @@ -59,6 +61,7 @@ def __init__(self, title="Composite plot", xmin=-500, xmax=500, ymin=-1, ymax=1, self.xscale = XScale(self) self.yscale = yScale(self) self.num_composites = 0 + self.composite_groups = [] def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary_color=None, i=None, opacity=None, smoothing=None, bp_shift=None, hide_sense=False, hide_anti=False, baseline=0): @@ -92,7 +95,7 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary scaled_occupancy = [value if (value := d * scale + baseline) > 0 else 0 for j, d in enumerate(smoothed_occupancy) if int(new_xdomain[j]) >= self.xmin and int(new_xdomain[j]) <= self.xmax] composite_fill_top = document.createElement("polygon") - composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") self.composite_group.appendChild(composite_fill_top) #Create outline @@ -125,7 +128,7 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary if not hide_anti: # Create top polygon composite_fill_top = document.createElement("polygon") - composite_fill_top.setAttribute("points", " ".join(sense_points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("points", " ".join(sense_points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") self.composite_group.appendChild(composite_fill_top) #Create trace @@ -146,7 +149,7 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary if not hide_anti: # Create polygon composite_fill_bottom = document.createElement("polygon") - composite_fill_bottom.setAttribute("points", " ".join(anti_points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") + composite_fill_bottom.setAttribute("points", " ".join(anti_points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") composite_fill_bottom.setAttribute("fill", "url(#composite-gradient-bottom" + str(i) + ")") self.composite_group.appendChild(composite_fill_bottom) #Create trace @@ -168,6 +171,139 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary self.super_group.appendChild(self.composite_group) return self.super_group + def plot_composite_group(self, composite_group): + document = dom.Document() + # Set parameters to global values if not specified + opacity = composite_group.opacity if composite_group.opacity is not None else self.opacity + smoothing = composite_group.smoothing if composite_group.smoothing is not None else self.smoothing + bp_shift = composite_group.bp_shift if composite_group.bp_shift is not None else self.bp_shift + i = self.num_composites + self.num_composites += 1 + # Set x domain as array of integers from xmin to xmax + xdomain = [i + composite_group.xmin for i in range(composite_group.xmax - composite_group.xmin + 1)] + if (self.combined): + # Calculate defined x domain after shifting + shifted_xdomain = [x for x in xdomain if x - bp_shift >= xdomain[0] and x - bp_shift <= xdomain[-1] + and x + bp_shift >= xdomain[0] and x + bp_shift <= xdomain[-1]] + shifted_sense = [composite_group.sense[j] for j in range(len(composite_group.sense)) if xdomain[j] + bp_shift >= shifted_xdomain[0] + and xdomain[j] + bp_shift <= shifted_xdomain[-1]] + shifted_anti = [composite_group.anti[j] for j in range(len(composite_group.anti)) if xdomain[j] + bp_shift >= shifted_xdomain[0] + and xdomain[j] + bp_shift <= shifted_xdomain[-1]] + # Add occupancy for sense and anti + combined_occupancy = [shifted_sense[j] + shifted_anti[j] for j in range(len(shifted_sense))] + # Smooth occupancy with moving average + new_xdomain, smoothed_occupancy = slidingWindow.sliding_window(shifted_xdomain, combined_occupancy, smoothing).values() + # Truncate x domain to x axis limits + truncated_xdomain = [x for x in new_xdomain if x >= self.xmin and x <= self.xmax] + # Truncate occupancy and scale by scale factor, adding baseline value + scaled_occupancy = [value if (value := d * composite_group.scale + composite_group.baseline) > 0 else 0 for j, d in enumerate(smoothed_occupancy) + if int(new_xdomain[j]) >= self.xmin and int(new_xdomain[j]) <= self.xmax] + composite_fill_top = document.createElement("polygon") + composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") + self.composite_group.appendChild(composite_fill_top) + #Create outline + wide_trace = document.createElement("path") + wide_trace.setAttribute("stroke-width", "1") + wide_trace.setAttribute("stroke", composite_group.color) + wide_trace.setAttribute("fill", "none") + wide_trace.setAttribute("d", "M" + "L".join(points)) + self.composite_group.appendChild(wide_trace) + if not self.color_trace: + wide_trace.setAttribute("stroke", "#FFFFFF") + narrow_trace = copy.deepcopy(wide_trace) + narrow_trace.setAttribute("stroke-width", "0.5") + narrow_trace.setAttribute("stroke", "#000000") + narrow_trace.setAttribute("d", "M" + "L".join(points)) + self.composite_group.appendChild(narrow_trace) + else: + # Smooth sense and anti occupancy with moving average + new_xdomain, smoothed_sense = slidingWindow.sliding_window(xdomain, composite_group.sense, smoothing).values() + smoothed_anti = list(slidingWindow.sliding_window(xdomain, composite_group.anti, smoothing).values())[1] + # Truncate x domain to x axis limits + truncated_sense_domain = [j for x in new_xdomain if (j := x + bp_shift) >= self.xmin and j <= self.xmax] + truncated_anti_domain = [j for x in new_xdomain if (j := x - bp_shift) >= self.xmin and j <= self.xmax] + # Truncate sense and anti occupancy and scale by scale factor + scaled_sense = [value if (value := d * composite_group.scale + composite_group.baseline) > 0 else 0 for j, d in enumerate(smoothed_sense) + if int(new_xdomain[j] + bp_shift) >= self.xmin and int(new_xdomain[j] + bp_shift) <= self.xmax] + scaled_anti = [value if (value := d * composite_group.scale + composite_group.baseline) > 0 else 0 for j, d in enumerate(smoothed_anti) + if int(new_xdomain[j] - bp_shift) >= self.xmin and int(new_xdomain[j] - bp_shift) <= self.xmax] + # Create sense trace and polygon if not hidden + if not composite_group.hide_anti: + # Create top polygon + composite_fill_top = document.createElement("polygon") + composite_fill_top.setAttribute("points", " ".join(sense_points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") + composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") + self.composite_group.appendChild(composite_fill_top) + #Create trace + top_wide_trace = document.createElement("path") + top_wide_trace.setAttribute("stroke-width", "1") + top_wide_trace.setAttribute("stroke", composite_group.color) + top_wide_trace.setAttribute("fill", "none") + top_wide_trace.setAttribute("d", "M" + "L".join(sense_points)) + self.composite_group.appendChild(top_wide_trace) + if not self.color_trace: + top_wide_trace.setAttribute("stroke", "#FFFFFF") + top_narrow_trace = copy.deepcopy(top_wide_trace) + top_narrow_trace.setAttribute("stroke-width", "0.5") + top_narrow_trace.setAttribute("stroke", "#000000") + top_narrow_trace.setAttribute("d", "M" + "L".join(sense_points)) + self.composite_group.appendChild(top_narrow_trace) + # Create anti trace and polygon if not hidden + if not composite_group.hide_anti: + # Create polygon + composite_fill_bottom = document.createElement("polygon") + composite_fill_bottom.setAttribute("points", " ".join(anti_points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") + composite_fill_bottom.setAttribute("fill", "url(#composite-gradient-bottom" + str(i) + ")") + self.composite_group.appendChild(composite_fill_bottom) + #Create trace + bottom_wide_trace = document.createElement("path") + bottom_wide_trace.setAttribute("stroke-width", "1") + bottom_wide_trace.setAttribute("stroke", composite_group.secondary_color) + bottom_wide_trace.setAttribute("fill", "none") + bottom_wide_trace.setAttribute("d", "M" + "L".join(anti_points)) + self.composite_group.appendChild(bottom_wide_trace) + if not self.color_trace: + bottom_wide_trace.setAttribute("stroke", "#FFFFFF") + bottom_narrow_trace = copy.deepcopy(bottom_wide_trace) + bottom_narrow_trace.setAttribute("stroke-width", "0.5") + bottom_narrow_trace.setAttribute("stroke", "#000000") + bottom_narrow_trace.setAttribute("d", "M" + "L".join(anti_points)) + self.composite_group.appendChild(bottom_narrow_trace) + self.generateGradients(opacity, i, composite_group.color, secondary_color=composite_group.secondary_color) + self.super_group.appendChild(self.gradients_group) + self.super_group.appendChild(self.composite_group) + return self.super_group + + def scale_axes(self, xmin=None, xmax=None, ymin=None, ymax=None): + self.xmin = xmin if xmin is not None else self.xmin + self.xmax = xmax if xmax is not None else self.xmax + self.ymin = ymin if ymin is not None else self.ymin + self.ymax = ymax if ymax is not None else self.ymax + self.xscale = XScale(self) + self.yscale = yScale(self) + + def autoscale_axes(self): + xmin = min([group.xmin for group in self.composite_groups]) + xmax = max([group.xmax for group in self.composite_groups]) + if self.combined: + ymin = 0 + ymax = round(max([(group.sense[i] + group.sense[i]) * group.scale for group in self.composite_groups for i in range(min(len(group.sense), len(group.anti)))]), 2) + else: + ymin = min([-val * group.scale for group in self.composite_groups for val in group.anti]) + ymax = max([val * group.scale for group in self.composite_groups for val in group.sense]) + self.scale_axes(xmin,xmax,ymin,ymax) + + def add_composite_group(self, composite_group): + if composite_group.name == None: + composite_group.name = self.num_composites + 1 + self.composite_groups.append(composite_group) + + def plot_composite_groups(self): + for group in self.composite_groups: + self.plot_composite_group(group) + return self.super_group + def generateGradients(self, opacity, i, color, secondary_color=None): # Creates DOM elements for top and bottom gradients secondary_color = secondary_color if secondary_color is not None else color diff --git a/python/plotter.py b/python/plotter.py index 7098d0b..474e6d8 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -1,15 +1,24 @@ import numpy as np import plot import composite +from composite import CompositeGroup import re import xml.dom.minidom as dom import argparse +import math import parseComposite document = dom.Document() -group = document.appendChild(document.createElement('g')) +group = document.appendChild(document.createElement('svg')) +group.setAttribute("xmlns", "http://www.w3.org/2000/svg") +group.setAttribute("id", "main-plot") +group.setAttribute("font-family", "Helvetica") +group.setAttribute("viewBox", "0 0 460 300") +group.setAttribute("style", "height: 50vh; max-width: 100%; overflow: hide;") +group.setAttribute("baseProfile", "full") def generateSVG(plot): + #Create title title = document.createElement('text') title.setAttribute("font-size", "16") title.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) @@ -19,6 +28,7 @@ def generateSVG(plot): title.setAttribute("style", "text-anchor: middle; cursor: pointer;") title.appendChild(document.createTextNode(plot.title)) + #Create labels for xmin and xmax xlabel = document.createElement('text') xlabel.setAttribute("font-size", "16") xlabel.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) @@ -28,21 +38,6 @@ def generateSVG(plot): xlabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") xlabel.appendChild(document.createTextNode(plot.xlabel)) - ylabel = document.createElement('text') - ylabel.setAttribute("font-size", "16") - ylabel.setAttribute("x", "12") - ylabel.setAttribute("y", str((plot.height + plot.margins.get('top') - plot.margins.get('bottom')) / 2)) - ylabel.setAttribute("label", "ylabel") - ylabel.setAttribute("id", "main-plot-ylabel") - ylabel.setAttribute("transform", "rotate(-90 12 147.5)") - ylabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") - ylabel.appendChild(document.createTextNode(plot.ylabel)) - - composite_group = document.createElement('g') - - legend = document.createElement('g') - legend.setAttribute("transform", "translate(" + str(plot.width - plot.margins.get("right") + 25) + " " + str(plot.margins.get("top")) + ")") - xmin = document.createElement('text') xmin.setAttribute("x", str(plot.margins.get("left"))) xmin.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) @@ -57,42 +52,234 @@ def generateSVG(plot): xmax.setAttribute("font-size", "14px") xmax.appendChild(document.createTextNode(str(plot.xmax))) - ymin = document.createElement('text') - ymin.setAttribute("x", "30") - ymin.setAttribute("y", str(plot.height - plot.margins.get("bottom"))) - ymin.setAttribute("text-anchor", "middle") - ymin.setAttribute("font-size", "14px") - ymin.appendChild(document.createTextNode(str(plot.ymin))) + #Create ylabel with exponent + ylabel = document.createElement('text') + ylabel.setAttribute("font-size", "16") + ylabel.setAttribute("x", "12") + ylabel.setAttribute("y", str((plot.height + plot.margins.get('top') - plot.margins.get('bottom')) / 2)) + ylabel.setAttribute("label", "ylabel") + ylabel.setAttribute("id", "main-plot-ylabel") + ylabel.setAttribute("transform", "rotate(-90 12 147.5)") + ylabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") + + round_exp = 1 - math.floor(math.log10(plot.ymax - plot.ymin)) + round_factor = 10 ** round_exp + print(round_factor) + exp_label = round_exp <= -2 or round_exp >= 2 + + if exp_label: + ylabel.appendChild(document.createTextNode(plot.ylabel + " X10")) + ylabel_suffix = document.createElement("tspan") + ylabel_suffix.setAttribute("font-size", "8px") + ylabel_suffix.setAttribute("baseline-shift", "super") + ylabel_suffix.appendChild(document.createTextNode(str(1 - round_exp))) + ylabel.appendChild(ylabel_suffix) + else: + ylabel.appendChild(document.createTextNode(plot.ylabel)) + + #Create ymin and ymax + if not plot.combined: + ymin = document.createElement('text') + ymin.setAttribute("x", "30") + ymin.setAttribute("y", str(plot.height - plot.margins.get("bottom"))) + ymin.setAttribute("text-anchor", "end") + ymin.setAttribute("font-size", "14px") + ymin.appendChild(document.createTextNode(str((round(plot.ymin, 2) * round_factor) / (10 if exp_label else round_factor)))) + group.appendChild(ymin) ymax = document.createElement('text') ymax.setAttribute("x", "30") ymax.setAttribute("y", str(plot.margins.get("top") + 10)) - ymax.setAttribute("text-anchor", "middle") + ymax.setAttribute("text-anchor", "end") ymax.setAttribute("font-size", "14px") - ymax.appendChild(document.createTextNode(str(plot.ymax))) + ymax.appendChild(document.createTextNode(str((round(plot.ymax, 2) * round_factor) / (10 if exp_label else round_factor)))) + #Create legend + group.appendChild(create_legend(plot)) + #Create vertical line at reference point + zero_line = document.createElement("line") + zero_line.setAttribute("stroke", "grey") + zero_line.setAttribute("opacity", "0.5") + zero_line.setAttribute("y1", str(plot.margins.get("top"))) + zero_line.setAttribute("y2", str(plot.height - plot.margins.get("bottom"))) + zero_line.setAttribute("x1", str(plot.xscale.get(0))) + zero_line.setAttribute("x2", str(plot.xscale.get(0))) + zero_line.setAttribute("stroke-dasharray", "5,5") + group.appendChild(zero_line) + + axis_left = axis("left", None, plot) + axis_right = axis("right", None, plot) + axis_bottom = axis("bottom", None, plot) + axis_top = axis("top", None, plot) + axis_middle = axis("middle", None, plot) + + group.appendChild(axis_left) + group.appendChild(axis_right) + group.appendChild(axis_bottom) + group.appendChild(axis_top) + group.appendChild(axis_middle) + group.appendChild(title) group.appendChild(xlabel) group.appendChild(ylabel) group.appendChild(xmin) group.appendChild(xmax) - group.appendChild(ymin) group.appendChild(ymax) -def main(): - return True +def axis(orient, scale, plot): + tickSpacing = 23.5 if orient == "left" or orient == "right" else 25 + tickSize = 6 if orient == "left" or orient == "top" else -6 + axis_group = document.createElement("g") + axis = document.createElement("line") + + bottom = plot.height - plot.margins.get('bottom') + top = plot.margins.get("top") + right = plot.width - (plot.margins.get('right')) + left = plot.margins.get("left") + + match orient: + case "left": + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(left)) + axis.setAttribute("y1", str(top)) + axis.setAttribute("y2", str(bottom)) + i = top + while i < bottom: + tick = document.createElement("line") + tick.setAttribute("y1", str(i)) + tick.setAttribute("y2", str(i)) + tick.setAttribute("x1", str(left)) + tick.setAttribute("x2", str(left + tickSize)) + axis_group.appendChild(tick) + i += tickSpacing + case "right": + axis.setAttribute("x1", str(right)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(top)) + axis.setAttribute("y2", str(bottom)) + i = top + while i < bottom: + tick = document.createElement("line") + tick.setAttribute("y1", str(i)) + tick.setAttribute("y2", str(i)) + tick.setAttribute("x1", str(right)) + tick.setAttribute("x2", str(right + tickSize)) + axis_group.appendChild(tick) + i += tickSpacing + case "bottom": + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(bottom)) + axis.setAttribute("y2", str(bottom)) + i = left + while i < right: + tick = document.createElement("line") + tick.setAttribute("y1", str(bottom)) + tick.setAttribute("y2", str(bottom + tickSize)) + tick.setAttribute("x1", str(i)) + tick.setAttribute("x2", str(i)) + axis_group.appendChild(tick) + i += tickSpacing + case "top": + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(top)) + axis.setAttribute("y2", str(top)) + i = left + while i < right: + tick = document.createElement("line") + tick.setAttribute("y1", str(top)) + tick.setAttribute("y2", str(top + tickSize)) + tick.setAttribute("x1", str(i)) + tick.setAttribute("x2", str(i)) + axis_group.appendChild(tick) + i += tickSpacing + case "middle": + if not plot.combined == True: + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(plot.yscale.get(0))) + axis.setAttribute("y2", str(plot.yscale.get(0))) + i = left + while i < right: + tick = document.createElement("line") + tick.setAttribute("y1", str(plot.yscale.get(0) - tickSize)) + tick.setAttribute("y2", str(plot.yscale.get(0) + tickSize)) + tick.setAttribute("x1", str(i)) + tick.setAttribute("x2", str(i)) + axis_group.appendChild(tick) + i += tickSpacing + axis_group.setAttribute("stroke", "black") + axis_group.appendChild(axis) + + return axis_group + +def create_legend(plot): + legend = document.createElement('g') + legend.setAttribute("transform", "translate(" + str(plot.width - plot.margins.get("right") + 25) + " " + str(plot.margins.get("top")) + ")") + i = 0 + for composite_group in plot.composite_groups: + legend_element = document.createElement("g") + legend_element.setAttribute("transform", "translate(0," + str(24 * i) + ")") + + legend_color_sense = document.createElement("polygon") + legend_color_sense.setAttribute("points", "0,0 15,0 15,15 0,15") + legend_color_sense.setAttribute("fill", composite_group.color) + legend_element.appendChild(legend_color_sense) + legend_color_anti = document.createElement("polygon") + legend_color_anti.setAttribute("points", "0,0 15,0 15,15 0,15") + legend_element.appendChild(legend_color_anti) + legend_color_anti.setAttribute("fill", composite_group.secondary_color) + legend_border = document.createElement("rect") + legend_border.setAttribute("width", "15") + legend_border.setAttribute("height", "15") + legend_border.setAttribute("stroke", "#000000") + legend_border.setAttribute("fill", "none") + legend_element.appendChild(legend_border) + + id = document.createElement("text") + id.setAttribute("x", "20") + id.setAttribute("y", "10") + id.setAttribute("font-size", "10") + id.appendChild(document.createTextNode(str(composite_group.name))) + legend_element.appendChild(id) + legend.appendChild(legend_element) + i += 1 + return legend +def main(): + return True if __name__ == "__main__": - p = plot.Plot(combined=False, color_trace=False, opacity=1, xmin=-500) + p = plot.Plot(combined=False, color_trace=False, opacity=1, xmin=-1000) parser = argparse.ArgumentParser() parser.add_argument("composites", nargs="+") + parser.add_argument("--names", nargs="+", default=None) + parser.add_argument("--colors", nargs="+", default=None) + parser.add_argument("--secondary-colors", nargs="+", default=None) + + # parser = argparse.ArgumentParser() + + # for i in range(0,2): + # sp = parser.add_subparsers(dest='sub{i}', required=False) + # spp = sp.add_parser("composite") + # spp.add_argument('--name', dest=f"name{i}", nargs=1) + args = parser.parse_args() + # print(args) + + composite_groups = [] + names = args.names if args.names != None else range(1, len(args.composites) + 1) + colors = args.colors if args.colors != None else ["#BFBFBF","#000000","#FF0000","#FF9100","#D7D700","#07E200","#00B0F0","#0007FF","#A700FF","#FF00D0"] + secondary_colors = args.secondary_colors + print(args.secondary_colors) + + i = 0 for g in args.composites: - composite_group = composite.CompositeGroup() + composite_group = CompositeGroup(name=names[i], color=colors[i % len(colors)]) composite_files = g.split("-") for c in composite_files: #Check if composite file contains multiple composites @@ -103,17 +290,15 @@ def main(): prefixes = parseComposite.get_prefixes_from_multiple_composites(c) composites = parseComposite.parse_multiple_composite(c, prefixes) composite_group.loadCompositeDict(composites) - group.appendChild(p.plot_composite(composite_group.xmin, composite_group.xmax, composite_group.sense, composite_group.anti, scale=15, color="#FF0000", secondary_color="#0000FF")) + p.add_composite_group(composite_group) + i += 1 + p.autoscale_axes() + group.appendChild(p.plot_composite_groups()) generateSVG(p) - if p.combined: - template = open("resources/combined_template.xml", "r").read() - else: - template = open("resources/template.xml", "r").read() with open("out.xml", 'w') as f: - f.write(template + "\n\t") + # f.write(template + "\n\t") group.writexml(f, addindent=' ', newl='\n') - f.write("") print(args.composites) From 65f784418ac941d6fb9d4485f92cf34afb48d8bf Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Fri, 10 May 2024 19:47:03 -0400 Subject: [PATCH 4/9] fixed confusing naming and finished parsing --- python/composite.py | 66 +++---- python/out.xml | 146 --------------- python/plot.py | 272 +++++++++++++++++---------- python/plotter.py | 393 ++++++++++++---------------------------- python/slidingWindow.py | 1 + 5 files changed, 315 insertions(+), 563 deletions(-) delete mode 100644 python/out.xml diff --git a/python/composite.py b/python/composite.py index 9b58b5b..f8a37ab 100644 --- a/python/composite.py +++ b/python/composite.py @@ -1,55 +1,53 @@ -import numpy as np import csv import xml.dom.minidom as dom import argparse import math import parseComposite -class Composite: +# Objected to store bare-bones composite data, can be used with plot_composite function +class SimpleComposite: def __init__(self, xmin=None, xmax=None, sense=[], anti=[], id=""): self.xmin = xmin self.xmax = xmax self.sense = sense self.anti = anti self.id = id - - def __str__(self): - return "Sense: " + str(self.sense) + "\nAnti: " + str(self.anti) + "\nXMin: " + str(self.xmin) + "\nXMax: " + str(self.xmax) + "\nID:" + str(self.id) -class CompositeGroup: +# Object to store composite data with options for plotting, similar to a settings row +class Composite: def __init__(self, scale=1, color=None, secondary_color=None, i=None, opacity=None, smoothing=None, bp_shift=None, hide_sense=False, hide_anti=False, baseline=0, name=None): + # Sets default values + self.scale = scale if scale is not None else 1 + self.color = color if color is not None else "#0000FF" + self.secondary_color = secondary_color if secondary_color is not None else color + self.baseline = baseline if baseline is not None else 0 self.xmin = 0 self.xmax = 0 self.sense = [] self.anti = [] - self.scale = scale - self.color = color - self.secondary_color = secondary_color if secondary_color is not None else color self.opacity = opacity self.smoothing = smoothing self.bp_shift = bp_shift self.hide_anti = hide_anti - self.baseline = baseline self.hide_sense = hide_sense - self.individual_composites = {} - self.files_loaded = len(self.individual_composites) + self.individual_files = {} + self.files_loaded = len(self.individual_files) self.name = name - - def loadComposite(self,composite: Composite): + # Adds a simple composite to the 'row' + def load_simple_composite(self,composite: SimpleComposite): # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain self.xmin = min(composite.xmin, self.xmin) self.xmax = max(composite.xmax, self.xmax) - if len(self.individual_composites) == 0: + if len(self.individual_files) == 0: self.sense = [0] * (composite.xmax - composite.xmin + 1) self.anti = [0] * (composite.xmax - composite.xmin + 1) else: - xmin = min([int(self.individual_composites[c].xmin) for c in self.individual_composites]) - xmax = max([int(self.individual_composites[c].xmax) for c in self.individual_composites]) + xmin = min([int(self.individual_files[c].xmin) for c in self.individual_files]) + xmax = max([int(self.individual_files[c].xmax) for c in self.individual_files]) prefix = [0] * (xmin - self.xmin) suffix = [0] * (self.xmax - xmax) self.sense = prefix + self.sense + suffix self.anti = prefix + self.anti + suffix - # Update sense and anti arrays j = composite.xmin - self.xmin while j <= composite.xmax - composite.xmin: @@ -57,25 +55,23 @@ def loadComposite(self,composite: Composite): self.sense[idx] += composite.sense[j] self.anti[idx] += composite.anti[j] j += 1 - - self.individual_composites[composite.id] = composite - - def loadCompositeDict(self,compositeDict: dict): + self.individual_files[composite.id] = composite + # Loads dictionary from parse_multiple_composites + def load_composite_dict(self,compositeDict: dict): for composite in compositeDict: # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain self.xmin = min(composite.xmin, self.xmin) self.xmax = max(composite.xmax, self.xmax) - if len(self.individual_composites) == 0: + if len(self.individual_files) == 0: self.sense = [0] * (composite.xmax - composite.xmin + 1) self.anti = [0] * (composite.xmax - composite.xmin + 1) else: - xmin = min([c.xmin for c in self.individual_composites]) - xmax = max([c.xmax for c in self.individual_composites]) + xmin = min([c.xmin for c in self.individual_files]) + xmax = max([c.xmax for c in self.individual_files]) prefix = [0] * (xmin - self.xmin) suffix = [0] * (self.xmax - xmax) self.sense = prefix + self.sense + suffix self.anti = prefix + self.anti + suffix - # Update sense and anti arrays j = composite.xmin - self.xmin while j <= composite.xmax - composite.xmin: @@ -83,20 +79,6 @@ def loadCompositeDict(self,compositeDict: dict): self.sense[idx] += composite.sense[j] self.anti[idx] += composite.anti[j] j += 1 - - self.individual_composites[composite.id] = composite - + self.individual_files[composite.id] = composite def __str__(self): - return str(self.individual_composites) - -def main(): - c = parseComposite.parseComposite("sample_composites/sample_1.out") - compositeGroup = CompositeGroup() - compositeGroup.loadComposite(c) - c2 = parseComposite.parseComposite("sample_composites/sample2.out.txt") - compositeGroup.loadComposite(c2) - print(compositeGroup) - - -if __name__ == "__main__": - main() \ No newline at end of file + return str(self.individual_files) \ No newline at end of file diff --git a/python/out.xml b/python/out.xml deleted file mode 100644 index 6a0fbb2..0000000 --- a/python/out.xml +++ /dev/null @@ -1,146 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.6 - - - - - - composite_one - - - - - - composite_two - - - - - - composite_three - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Composite plot - Position (bp) - - Occupancy (AU) X10 - -1 - - -549 - 550 - 0.6 - diff --git a/python/plot.py b/python/plot.py index e7863ac..6900d17 100644 --- a/python/plot.py +++ b/python/plot.py @@ -1,71 +1,48 @@ -import numpy as np -import re import xml.dom.minidom as dom -import argparse import copy import slidingWindow import math -class Composite: - pass +document = dom.Document() -class XScale: - def __init__(self, plot): - self.plot = plot - self.domain = [plot.xmin, plot.xmax, plot.xmax - plot.xmin] - self.range = [plot.margins.get('left'), plot.width - plot.margins.get('right'), plot.width - (plot.margins.get('right') + plot.margins.get('left'))] - self.zero = (plot.width - (plot.margins.get('right') + plot.margins.get('left'))) * (abs(plot.xmin) / (abs(plot.xmin) + abs(plot.xmax))) + plot.margins.get('left') - - def get(self, value): - return (self.range[2] / self.domain[2]) * value + self.zero - - def inverse(self, value): - return (value - self.zero) * (self.domain[2] / self.range[2]) - -class yScale: - def __init__(self, plot): - self.domain = [plot.ymin, plot.ymax, abs(plot.ymax) + abs(plot.ymin)] - self.range = [plot.margins.get('top'), plot.height - plot.margins.get('bottom'), plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))] - self.zero = (plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))) * (0.5) + plot.margins.get('top') if plot.combined is False else self.range[1] - - def get(self, value): - return self.zero - (self.range[2] / self.domain[2]) * value - - def inverse(self, value): - return (value - self.zero) * (self.domain[2] / self.range[2]) - +# Class that generates composite and reference lines svg elements class Plot: - def __init__(self, title="Composite plot", xmin=-500, xmax=500, ymin=-1, ymax=1, xlabel="Position (bp)", ylabel="Occupancy (AU)", - opacity=1, smoothing=7, bp_shift=0, combined=False, color_trace=False, show_legend=True): - self.title = title - self.xmin = xmin - self.xmax = xmax - self.ymin = ymin - self.ymax = ymax - self.xlabel = xlabel - self.ylabel = ylabel + def __init__(self, title=None, xmin=None, xmax=None, ymin=None, ymax=None, xlabel=None, ylabel=None, + opacity=None, smoothing=None, bp_shift=None, combined=False, color_trace=False, hide_legend=True): + # Set variables to defaults if argument passed into constructor was None + self.title = title if title is not None else "Composite plot" + self.xmin = xmin if xmin is not None else -500 + self.xmax = xmax if xmax is not None else 500 + self.ymin = ymin if ymin is not None else -1 + self.ymax = ymax if ymax is not None else 1 + self.xlabel = xlabel if xlabel is not None else "Position (bp)" + self.ylabel = ylabel if ylabel is not None else "Occupancy (AU)" + self.opacity = opacity if opacity is not None else 1 + self.smoothing = smoothing if smoothing is not None else 7 + self.bp_shift = bp_shift if bp_shift is not None else 0 + self.combined = combined + self.color_trace = color_trace + self.hide_legend = hide_legend + # Set dimensions to same constants as plotter self.width = 460 self.height = 300 self.margins = {'top': 30, 'right': 170, 'bottom': 35, 'left': 40} - self.opacity = opacity - self.smoothing = smoothing - self.bp_shift = bp_shift - self.combined = combined - self.color_trace = color_trace - self.show_legend = show_legend - document = dom.Document() + # Create groups for adding composites and reference lines + self.plot = document.createElement("g") self.composite_group = document.createElement("g") self.composite_group.setAttribute("class", "composite plotted") self.gradients_group = document.createElement("defs") - self.super_group = document.createElement("g") + self.reference_group = document.createElement("g") self.xscale = XScale(self) - self.yscale = yScale(self) + self.yscale = YScale(self) self.num_composites = 0 - self.composite_groups = [] + self.composites = [] + self.styles ={"dashed" : "5,5", + "solid" : "0", + "dotted" : "2,1"} - + # Creates a composite svg element from separate sense and anti arrays - mimics plot_composite from plotter def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary_color=None, i=None, opacity=None, smoothing=None, bp_shift=None, hide_sense=False, hide_anti=False, baseline=0): - document = dom.Document() # Set parameters to global values if not specified opacity = opacity if opacity is not None else self.opacity smoothing = smoothing if smoothing is not None else self.smoothing @@ -167,27 +144,26 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary bottom_narrow_trace.setAttribute("d", "M" + "L".join(anti_points)) self.composite_group.appendChild(bottom_narrow_trace) self.generateGradients(opacity, i, color, secondary_color=secondary_color) - self.super_group.appendChild(self.gradients_group) - self.super_group.appendChild(self.composite_group) - return self.super_group + self.plot.appendChild(self.gradients_group) + self.plot.appendChild(self.composite_group) - def plot_composite_group(self, composite_group): - document = dom.Document() + # Creates a composite svg element from a composite_group object, like plotting a row form the settings table + def plot_composite(self, composite): # Set parameters to global values if not specified - opacity = composite_group.opacity if composite_group.opacity is not None else self.opacity - smoothing = composite_group.smoothing if composite_group.smoothing is not None else self.smoothing - bp_shift = composite_group.bp_shift if composite_group.bp_shift is not None else self.bp_shift + opacity = composite.opacity if composite.opacity is not None else self.opacity + smoothing = composite.smoothing if composite.smoothing is not None else self.smoothing + bp_shift = composite.bp_shift if composite.bp_shift is not None else self.bp_shift i = self.num_composites self.num_composites += 1 # Set x domain as array of integers from xmin to xmax - xdomain = [i + composite_group.xmin for i in range(composite_group.xmax - composite_group.xmin + 1)] + xdomain = [i + composite.xmin for i in range(composite.xmax - composite.xmin + 1)] if (self.combined): # Calculate defined x domain after shifting shifted_xdomain = [x for x in xdomain if x - bp_shift >= xdomain[0] and x - bp_shift <= xdomain[-1] and x + bp_shift >= xdomain[0] and x + bp_shift <= xdomain[-1]] - shifted_sense = [composite_group.sense[j] for j in range(len(composite_group.sense)) if xdomain[j] + bp_shift >= shifted_xdomain[0] + shifted_sense = [composite.sense[j] for j in range(len(composite.sense)) if xdomain[j] + bp_shift >= shifted_xdomain[0] and xdomain[j] + bp_shift <= shifted_xdomain[-1]] - shifted_anti = [composite_group.anti[j] for j in range(len(composite_group.anti)) if xdomain[j] + bp_shift >= shifted_xdomain[0] + shifted_anti = [composite.anti[j] for j in range(len(composite.anti)) if xdomain[j] + bp_shift >= shifted_xdomain[0] and xdomain[j] + bp_shift <= shifted_xdomain[-1]] # Add occupancy for sense and anti combined_occupancy = [shifted_sense[j] + shifted_anti[j] for j in range(len(shifted_sense))] @@ -196,16 +172,16 @@ def plot_composite_group(self, composite_group): # Truncate x domain to x axis limits truncated_xdomain = [x for x in new_xdomain if x >= self.xmin and x <= self.xmax] # Truncate occupancy and scale by scale factor, adding baseline value - scaled_occupancy = [value if (value := d * composite_group.scale + composite_group.baseline) > 0 else 0 for j, d in enumerate(smoothed_occupancy) + scaled_occupancy = [value if (value := d * composite.scale + composite.baseline) > 0 else 0 for j, d in enumerate(smoothed_occupancy) if int(new_xdomain[j]) >= self.xmin and int(new_xdomain[j]) <= self.xmax] composite_fill_top = document.createElement("polygon") composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") - self.composite_group.appendChild(composite_fill_top) + self.composite.appendChild(composite_fill_top) #Create outline wide_trace = document.createElement("path") wide_trace.setAttribute("stroke-width", "1") - wide_trace.setAttribute("stroke", composite_group.color) + wide_trace.setAttribute("stroke", composite.color) wide_trace.setAttribute("fill", "none") wide_trace.setAttribute("d", "M" + "L".join(points)) self.composite_group.appendChild(wide_trace) @@ -218,18 +194,18 @@ def plot_composite_group(self, composite_group): self.composite_group.appendChild(narrow_trace) else: # Smooth sense and anti occupancy with moving average - new_xdomain, smoothed_sense = slidingWindow.sliding_window(xdomain, composite_group.sense, smoothing).values() - smoothed_anti = list(slidingWindow.sliding_window(xdomain, composite_group.anti, smoothing).values())[1] + new_xdomain, smoothed_sense = slidingWindow.sliding_window(xdomain, composite.sense, smoothing).values() + smoothed_anti = list(slidingWindow.sliding_window(xdomain, composite.anti, smoothing).values())[1] # Truncate x domain to x axis limits truncated_sense_domain = [j for x in new_xdomain if (j := x + bp_shift) >= self.xmin and j <= self.xmax] truncated_anti_domain = [j for x in new_xdomain if (j := x - bp_shift) >= self.xmin and j <= self.xmax] # Truncate sense and anti occupancy and scale by scale factor - scaled_sense = [value if (value := d * composite_group.scale + composite_group.baseline) > 0 else 0 for j, d in enumerate(smoothed_sense) + scaled_sense = [value if (value := d * composite.scale + composite.baseline) > 0 else 0 for j, d in enumerate(smoothed_sense) if int(new_xdomain[j] + bp_shift) >= self.xmin and int(new_xdomain[j] + bp_shift) <= self.xmax] - scaled_anti = [value if (value := d * composite_group.scale + composite_group.baseline) > 0 else 0 for j, d in enumerate(smoothed_anti) + scaled_anti = [value if (value := d * composite.scale + composite.baseline) > 0 else 0 for j, d in enumerate(smoothed_anti) if int(new_xdomain[j] - bp_shift) >= self.xmin and int(new_xdomain[j] - bp_shift) <= self.xmax] # Create sense trace and polygon if not hidden - if not composite_group.hide_anti: + if not composite.hide_anti: # Create top polygon composite_fill_top = document.createElement("polygon") composite_fill_top.setAttribute("points", " ".join(sense_points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") @@ -238,7 +214,7 @@ def plot_composite_group(self, composite_group): #Create trace top_wide_trace = document.createElement("path") top_wide_trace.setAttribute("stroke-width", "1") - top_wide_trace.setAttribute("stroke", composite_group.color) + top_wide_trace.setAttribute("stroke", composite.color) top_wide_trace.setAttribute("fill", "none") top_wide_trace.setAttribute("d", "M" + "L".join(sense_points)) self.composite_group.appendChild(top_wide_trace) @@ -250,7 +226,7 @@ def plot_composite_group(self, composite_group): top_narrow_trace.setAttribute("d", "M" + "L".join(sense_points)) self.composite_group.appendChild(top_narrow_trace) # Create anti trace and polygon if not hidden - if not composite_group.hide_anti: + if not composite.hide_anti: # Create polygon composite_fill_bottom = document.createElement("polygon") composite_fill_bottom.setAttribute("points", " ".join(anti_points := [f"{self.xscale.get(d)},{self.yscale.get(-scaled_anti[j])}" for j, d in enumerate(truncated_anti_domain)]) + f" {self.xscale.get(truncated_anti_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_anti_domain[0])},{self.yscale.get(0)}") @@ -259,7 +235,7 @@ def plot_composite_group(self, composite_group): #Create trace bottom_wide_trace = document.createElement("path") bottom_wide_trace.setAttribute("stroke-width", "1") - bottom_wide_trace.setAttribute("stroke", composite_group.secondary_color) + bottom_wide_trace.setAttribute("stroke", composite.secondary_color) bottom_wide_trace.setAttribute("fill", "none") bottom_wide_trace.setAttribute("d", "M" + "L".join(anti_points)) self.composite_group.appendChild(bottom_wide_trace) @@ -270,45 +246,130 @@ def plot_composite_group(self, composite_group): bottom_narrow_trace.setAttribute("stroke", "#000000") bottom_narrow_trace.setAttribute("d", "M" + "L".join(anti_points)) self.composite_group.appendChild(bottom_narrow_trace) - self.generateGradients(opacity, i, composite_group.color, secondary_color=composite_group.secondary_color) - self.super_group.appendChild(self.gradients_group) - self.super_group.appendChild(self.composite_group) - return self.super_group + self.generateGradients(opacity, i, composite.color, secondary_color=composite.secondary_color) + self.plot.appendChild(self.gradients_group) + self.plot.appendChild(self.composite_group) + # Changes values and updates scale objects def scale_axes(self, xmin=None, xmax=None, ymin=None, ymax=None): self.xmin = xmin if xmin is not None else self.xmin self.xmax = xmax if xmax is not None else self.xmax self.ymin = ymin if ymin is not None else self.ymin self.ymax = ymax if ymax is not None else self.ymax self.xscale = XScale(self) - self.yscale = yScale(self) + self.yscale = YScale(self) - def autoscale_axes(self): - xmin = min([group.xmin for group in self.composite_groups]) - xmax = max([group.xmax for group in self.composite_groups]) + # Finds the max/min x and y values from composites on plot and scales axes accordingly + def autoscale_axes(self, allow_shrink): + xmin = min([group.xmin for group in self.composites]) + xmax = max([group.xmax for group in self.composites]) if self.combined: ymin = 0 - ymax = round(max([(group.sense[i] + group.sense[i]) * group.scale for group in self.composite_groups for i in range(min(len(group.sense), len(group.anti)))]), 2) + ymax = round(max([(group.sense[i] + group.sense[i]) * group.scale for group in self.composites for i in range(min(len(group.sense), len(group.anti)))]), 2) else: - ymin = min([-val * group.scale for group in self.composite_groups for val in group.anti]) - ymax = max([val * group.scale for group in self.composite_groups for val in group.sense]) - self.scale_axes(xmin,xmax,ymin,ymax) + ymin = min([-val * group.scale for group in self.composites for val in group.anti]) + ymax = max([val * group.scale for group in self.composites for val in group.sense]) + self.scale_axes(xmin,xmax,ymin if allow_shrink else None,ymax if allow_shrink else None) + # Adds composite group object to plot def add_composite_group(self, composite_group): if composite_group.name == None: composite_group.name = self.num_composites + 1 - self.composite_groups.append(composite_group) + self.composites.append(composite_group) - def plot_composite_groups(self): - for group in self.composite_groups: - self.plot_composite_group(group) - return self.super_group + # Plots all composites on plot + def plot_composites(self): + for group in self.composites: + self.plot_composite(group) + return self.plot + + # Adds reference lines to plot + def plot_reference_line(self, axis=None, val=None, style=None, color=None, opacity=None): + # Sets default values for reference lines + axis = axis if axis is not None else "x" + val = val if val is not None else 0 + style = style if style is not None else "dashed" + color = color if color is not None else "#FF0000" + opacity = opacity if opacity is not None else 1 + bottom = self.height - self.margins.get('bottom') + top = self.margins.get("top") + right = self.width - (self.margins.get('right')) + left = self.margins.get("left") + # Draws reference lines on plot + line = document.createElement("line") + label = document.createElement("text") + if axis == "x": + val = int(val) + line = document.createElement("line") + line.setAttribute("x1", str(self.xscale.get(val))) + line.setAttribute("x2", str(self.xscale.get(val))) + line.setAttribute("y1", str(top)) + line.setAttribute("y2", str(bottom)) + label.setAttribute("x", str(self.xscale.get(val) - 4)) + label.setAttribute("y", str(bottom + 8)) + label.appendChild(document.createTextNode(str(val))) + elif axis == "y": + line = document.createElement("line") + line.setAttribute("x1", str(left)) + line.setAttribute("x2", str(right)) + line.setAttribute("y1", str(self.yscale.get(val))) + line.setAttribute("y2", str(self.yscale.get(val))) + label.setAttribute("x", str(right + 5)) + label.setAttribute("y", str(self.yscale.get(val) + 4)) + label.appendChild(document.createTextNode(str(val))) + line.setAttribute("stroke-dasharray", self.styles.get(style)) + line.setAttribute("stroke-width", "1") + line.setAttribute("stroke", color) + line.setAttribute("opacity", str(opacity)) + label.setAttribute("text-align", "middle") + label.setAttribute("fill", color) + label.setAttribute("font-size", "8px") + self.reference_group.appendChild(line) + self.reference_group.appendChild(label) + self.plot.appendChild(self.reference_group) + + # Creates legend for plot + def create_legend(self): + if not self.hide_legend: + legend = document.createElement('g') + legend.setAttribute("transform", "translate(" + str(self.width - self.margins.get("right") + 25) + " " + str(self.margins.get("top")) + ")") + i = 0 + for composite_group in self.composites: + # Creates legend entries for each composite + legend_element = document.createElement("g") + legend_element.setAttribute("transform", "translate(0," + str(24 * i) + ")") + legend_color_sense = document.createElement("polygon") + legend_color_sense.setAttribute("points", "0,0 15,0 15,15 0,15") + legend_color_sense.setAttribute("fill", composite_group.color) + legend_element.appendChild(legend_color_sense) + legend_color_anti = document.createElement("polygon") + legend_color_anti.setAttribute("points", "0,0 15,0 15,15 0,15") + legend_element.appendChild(legend_color_anti) + legend_color_anti.setAttribute("fill", composite_group.secondary_color) + legend_border = document.createElement("rect") + legend_border.setAttribute("width", "15") + legend_border.setAttribute("height", "15") + legend_border.setAttribute("stroke", "#000000") + legend_border.setAttribute("fill", "none") + legend_element.appendChild(legend_border) + id = document.createElement("text") + id.setAttribute("x", "20") + id.setAttribute("y", "10") + id.setAttribute("font-size", "10") + id.appendChild(document.createTextNode(str(composite_group.name))) + legend_element.appendChild(id) + legend.appendChild(legend_element) + i += 1 + self.plot.appendChild(legend) + + # Returns svg group with all composites and reference lines + def get_plot(self): + return self.plot def generateGradients(self, opacity, i, color, secondary_color=None): # Creates DOM elements for top and bottom gradients secondary_color = secondary_color if secondary_color is not None else color - - document = dom.Document() + # Generates top gradient composite_gradient_top = document.createElement("linearGradient") composite_gradient_top.setAttribute("class", "composite-gradient-top") composite_gradient_top.setAttribute("x1", "0%") @@ -327,7 +388,7 @@ def generateGradients(self, opacity, i, color, secondary_color=None): composite_gradient_top.appendChild(top_stop_one) composite_gradient_top.appendChild(top_stop_two) self.gradients_group.appendChild(composite_gradient_top) - + # Generates bottom gradient composite_gradient_bottom = document.createElement("linearGradient") composite_gradient_bottom.setAttribute("class", "composite-gradient-bottom") composite_gradient_bottom.setAttribute("x1", "0%") @@ -347,3 +408,28 @@ def generateGradients(self, opacity, i, color, secondary_color=None): composite_gradient_bottom.appendChild(bottom_stop_two) self.gradients_group.appendChild(composite_gradient_bottom) +# Class that mimics d3 scaleLinear() for x-axis of plot +class XScale: + def __init__(self, plot): + self.plot = plot + self.domain = [plot.xmin, plot.xmax, plot.xmax - plot.xmin] + self.range = [plot.margins.get('left'), plot.width - plot.margins.get('right'), plot.width - (plot.margins.get('right') + plot.margins.get('left'))] + self.zero = (plot.width - (plot.margins.get('right') + plot.margins.get('left'))) * (abs(plot.xmin) / (abs(plot.xmin) + abs(plot.xmax))) + plot.margins.get('left') + # Returns position given bp + def get(self, value): + return (self.range[2] / self.domain[2]) * value + self.zero + # Returns bp given position + def inverse(self, value): + return (value - self.zero) * (self.domain[2] / self.range[2]) +# Class that mimics d3 scaleLinear() for y-axis of plot +class YScale: + def __init__(self, plot): + self.domain = [plot.ymin, plot.ymax, abs(plot.ymax) + abs(plot.ymin)] + self.range = [plot.margins.get('top'), plot.height - plot.margins.get('bottom'), plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))] + self.zero = (plot.height - (plot.margins.get('top') + plot.margins.get('bottom'))) * (0.5) + plot.margins.get('top') if plot.combined is False else self.range[1] + # Returns position on svg given occupancy + def get(self, value): + return self.zero - (self.range[2] / self.domain[2]) * value + # Returns occupancy given position + def inverse(self, value): + return (value - self.zero) * (self.domain[2] / self.range[2]) diff --git a/python/plotter.py b/python/plotter.py index 474e6d8..7978509 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -1,304 +1,133 @@ -import numpy as np import plot import composite -from composite import CompositeGroup +from composite import Composite +from composite import SimpleComposite import re import xml.dom.minidom as dom import argparse import math import parseComposite +import sys +from enum import Enum +import svgFactory document = dom.Document() -group = document.appendChild(document.createElement('svg')) -group.setAttribute("xmlns", "http://www.w3.org/2000/svg") -group.setAttribute("id", "main-plot") -group.setAttribute("font-family", "Helvetica") -group.setAttribute("viewBox", "0 0 460 300") -group.setAttribute("style", "height: 50vh; max-width: 100%; overflow: hide;") -group.setAttribute("baseProfile", "full") - -def generateSVG(plot): - #Create title - title = document.createElement('text') - title.setAttribute("font-size", "16") - title.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) - title.setAttribute("y", "20") - title.setAttribute("label", "title") - title.setAttribute("id", "main-plot-title") - title.setAttribute("style", "text-anchor: middle; cursor: pointer;") - title.appendChild(document.createTextNode(plot.title)) - - #Create labels for xmin and xmax - xlabel = document.createElement('text') - xlabel.setAttribute("font-size", "16") - xlabel.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) - xlabel.setAttribute("y", str(plot.height - 5)) - xlabel.setAttribute("label", "xlabel") - xlabel.setAttribute("id", "main-plot-xlabel") - xlabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") - xlabel.appendChild(document.createTextNode(plot.xlabel)) - - xmin = document.createElement('text') - xmin.setAttribute("x", str(plot.margins.get("left"))) - xmin.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) - xmin.setAttribute("text-anchor", "middle") - xmin.setAttribute("font-size", "14px") - xmin.appendChild(document.createTextNode(str(plot.xmin))) - - xmax = document.createElement('text') - xmax.setAttribute("x", str(plot.width - plot.margins.get("right"))) - xmax.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) - xmax.setAttribute("text-anchor", "middle") - xmax.setAttribute("font-size", "14px") - xmax.appendChild(document.createTextNode(str(plot.xmax))) - - #Create ylabel with exponent - ylabel = document.createElement('text') - ylabel.setAttribute("font-size", "16") - ylabel.setAttribute("x", "12") - ylabel.setAttribute("y", str((plot.height + plot.margins.get('top') - plot.margins.get('bottom')) / 2)) - ylabel.setAttribute("label", "ylabel") - ylabel.setAttribute("id", "main-plot-ylabel") - ylabel.setAttribute("transform", "rotate(-90 12 147.5)") - ylabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") - - round_exp = 1 - math.floor(math.log10(plot.ymax - plot.ymin)) - round_factor = 10 ** round_exp - print(round_factor) - exp_label = round_exp <= -2 or round_exp >= 2 - - if exp_label: - ylabel.appendChild(document.createTextNode(plot.ylabel + " X10")) - ylabel_suffix = document.createElement("tspan") - ylabel_suffix.setAttribute("font-size", "8px") - ylabel_suffix.setAttribute("baseline-shift", "super") - ylabel_suffix.appendChild(document.createTextNode(str(1 - round_exp))) - ylabel.appendChild(ylabel_suffix) - else: - ylabel.appendChild(document.createTextNode(plot.ylabel)) - - #Create ymin and ymax - if not plot.combined: - ymin = document.createElement('text') - ymin.setAttribute("x", "30") - ymin.setAttribute("y", str(plot.height - plot.margins.get("bottom"))) - ymin.setAttribute("text-anchor", "end") - ymin.setAttribute("font-size", "14px") - ymin.appendChild(document.createTextNode(str((round(plot.ymin, 2) * round_factor) / (10 if exp_label else round_factor)))) - group.appendChild(ymin) - - ymax = document.createElement('text') - ymax.setAttribute("x", "30") - ymax.setAttribute("y", str(plot.margins.get("top") + 10)) - ymax.setAttribute("text-anchor", "end") - ymax.setAttribute("font-size", "14px") - ymax.appendChild(document.createTextNode(str((round(plot.ymax, 2) * round_factor) / (10 if exp_label else round_factor)))) - - #Create legend - group.appendChild(create_legend(plot)) - - #Create vertical line at reference point - zero_line = document.createElement("line") - zero_line.setAttribute("stroke", "grey") - zero_line.setAttribute("opacity", "0.5") - zero_line.setAttribute("y1", str(plot.margins.get("top"))) - zero_line.setAttribute("y2", str(plot.height - plot.margins.get("bottom"))) - zero_line.setAttribute("x1", str(plot.xscale.get(0))) - zero_line.setAttribute("x2", str(plot.xscale.get(0))) - zero_line.setAttribute("stroke-dasharray", "5,5") - group.appendChild(zero_line) - - axis_left = axis("left", None, plot) - axis_right = axis("right", None, plot) - axis_bottom = axis("bottom", None, plot) - axis_top = axis("top", None, plot) - axis_middle = axis("middle", None, plot) - - group.appendChild(axis_left) - group.appendChild(axis_right) - group.appendChild(axis_bottom) - group.appendChild(axis_top) - group.appendChild(axis_middle) - - group.appendChild(title) - group.appendChild(xlabel) - group.appendChild(ylabel) - group.appendChild(xmin) - group.appendChild(xmax) - group.appendChild(ymax) - -def axis(orient, scale, plot): - tickSpacing = 23.5 if orient == "left" or orient == "right" else 25 - tickSize = 6 if orient == "left" or orient == "top" else -6 - axis_group = document.createElement("g") - axis = document.createElement("line") - - bottom = plot.height - plot.margins.get('bottom') - top = plot.margins.get("top") - right = plot.width - (plot.margins.get('right')) - left = plot.margins.get("left") - - match orient: - case "left": - axis.setAttribute("x1", str(left)) - axis.setAttribute("x2", str(left)) - axis.setAttribute("y1", str(top)) - axis.setAttribute("y2", str(bottom)) - i = top - while i < bottom: - tick = document.createElement("line") - tick.setAttribute("y1", str(i)) - tick.setAttribute("y2", str(i)) - tick.setAttribute("x1", str(left)) - tick.setAttribute("x2", str(left + tickSize)) - axis_group.appendChild(tick) - i += tickSpacing - case "right": - axis.setAttribute("x1", str(right)) - axis.setAttribute("x2", str(right)) - axis.setAttribute("y1", str(top)) - axis.setAttribute("y2", str(bottom)) - i = top - while i < bottom: - tick = document.createElement("line") - tick.setAttribute("y1", str(i)) - tick.setAttribute("y2", str(i)) - tick.setAttribute("x1", str(right)) - tick.setAttribute("x2", str(right + tickSize)) - axis_group.appendChild(tick) - i += tickSpacing - case "bottom": - axis.setAttribute("x1", str(left)) - axis.setAttribute("x2", str(right)) - axis.setAttribute("y1", str(bottom)) - axis.setAttribute("y2", str(bottom)) - i = left - while i < right: - tick = document.createElement("line") - tick.setAttribute("y1", str(bottom)) - tick.setAttribute("y2", str(bottom + tickSize)) - tick.setAttribute("x1", str(i)) - tick.setAttribute("x2", str(i)) - axis_group.appendChild(tick) - i += tickSpacing - case "top": - axis.setAttribute("x1", str(left)) - axis.setAttribute("x2", str(right)) - axis.setAttribute("y1", str(top)) - axis.setAttribute("y2", str(top)) - i = left - while i < right: - tick = document.createElement("line") - tick.setAttribute("y1", str(top)) - tick.setAttribute("y2", str(top + tickSize)) - tick.setAttribute("x1", str(i)) - tick.setAttribute("x2", str(i)) - axis_group.appendChild(tick) - i += tickSpacing - case "middle": - if not plot.combined == True: - axis.setAttribute("x1", str(left)) - axis.setAttribute("x2", str(right)) - axis.setAttribute("y1", str(plot.yscale.get(0))) - axis.setAttribute("y2", str(plot.yscale.get(0))) - i = left - while i < right: - tick = document.createElement("line") - tick.setAttribute("y1", str(plot.yscale.get(0) - tickSize)) - tick.setAttribute("y2", str(plot.yscale.get(0) + tickSize)) - tick.setAttribute("x1", str(i)) - tick.setAttribute("x2", str(i)) - axis_group.appendChild(tick) - i += tickSpacing - axis_group.setAttribute("stroke", "black") - axis_group.appendChild(axis) - - return axis_group - -def create_legend(plot): - legend = document.createElement('g') - legend.setAttribute("transform", "translate(" + str(plot.width - plot.margins.get("right") + 25) + " " + str(plot.margins.get("top")) + ")") - i = 0 - for composite_group in plot.composite_groups: - legend_element = document.createElement("g") - legend_element.setAttribute("transform", "translate(0," + str(24 * i) + ")") - - legend_color_sense = document.createElement("polygon") - legend_color_sense.setAttribute("points", "0,0 15,0 15,15 0,15") - legend_color_sense.setAttribute("fill", composite_group.color) - legend_element.appendChild(legend_color_sense) - legend_color_anti = document.createElement("polygon") - legend_color_anti.setAttribute("points", "0,0 15,0 15,15 0,15") - legend_element.appendChild(legend_color_anti) - legend_color_anti.setAttribute("fill", composite_group.secondary_color) - legend_border = document.createElement("rect") - legend_border.setAttribute("width", "15") - legend_border.setAttribute("height", "15") - legend_border.setAttribute("stroke", "#000000") - legend_border.setAttribute("fill", "none") - legend_element.appendChild(legend_border) - - id = document.createElement("text") - id.setAttribute("x", "20") - id.setAttribute("y", "10") - id.setAttribute("font-size", "10") - id.appendChild(document.createTextNode(str(composite_group.name))) - legend_element.appendChild(id) - legend.appendChild(legend_element) - i += 1 - return legend - def main(): return True if __name__ == "__main__": - p = plot.Plot(combined=False, color_trace=False, opacity=1, xmin=-1000) - - parser = argparse.ArgumentParser() - parser.add_argument("composites", nargs="+") - parser.add_argument("--names", nargs="+", default=None) - parser.add_argument("--colors", nargs="+", default=None) - parser.add_argument("--secondary-colors", nargs="+", default=None) - - # parser = argparse.ArgumentParser() - - # for i in range(0,2): - # sp = parser.add_subparsers(dest='sub{i}', required=False) - # spp = sp.add_parser("composite") - # spp.add_argument('--name', dest=f"name{i}", nargs=1) - - args = parser.parse_args() - # print(args) - - composite_groups = [] - names = args.names if args.names != None else range(1, len(args.composites) + 1) - colors = args.colors if args.colors != None else ["#BFBFBF","#000000","#FF0000","#FF9100","#D7D700","#07E200","#00B0F0","#0007FF","#A700FF","#FF00D0"] - secondary_colors = args.secondary_colors - print(args.secondary_colors) - + # Remove 'plotter' from sys.argv + sys.argv.pop(0) + # Load subcommands into appropriate arrays + i = -1 + k = -1 + composite_commands = [] + ref_line_commands = [] + plot_command = "" + current = "composite" + for word in sys.argv: + print(word) + if word == "composite": + i += 1 + composite_commands.append("") + current = "composite" + elif word == "reference-line": + k += 1 + ref_line_commands.append("") + current = "ref" + elif word == "plot": + current = "plot" + elif current == "composite": + composite_commands[i] += f" {word}" + elif current == "ref": + ref_line_commands[k] += f" {word}" + elif current == "plot": + plot_command += f" {word}" + # Create parser for plot subcommand + plot_parser = argparse.ArgumentParser() + plot_parser.add_argument("--smoothing", type=float) + plot_parser.add_argument("--bp-shift", type=int) + plot_parser.add_argument("--opacity", type=float) + plot_parser.add_argument("--title") + plot_parser.add_argument("--xmin",type=int) + plot_parser.add_argument("--xmax",type=int) + plot_parser.add_argument("--xlabel", nargs="+") + plot_parser.add_argument("--ymin", type=int) + plot_parser.add_argument("--ymax", type=int) + plot_parser.add_argument("--ylabel", nargs="+") + plot_parser.add_argument("--color-trace", action="store_true", default=False) + plot_parser.add_argument("--combined", action="store_true", default=False) + plot_parser.add_argument("--hide-legend", action="store_false", default=True) + plot_parser.add_argument("--no-resize", action="store_true", default=False) + plot_parser.add_argument("--no-shrink", action="store_true", default=False) + plot_parser.add_argument("--reference-line", nargs=3, action='append') + plot_parser.add_argument("--out") + # Create plot based on plot subcommand, default values in Plot class will be used if argument is not specified + plot_args = plot_parser.parse_args(plot_command.split()) + p = plot.Plot(title=plot_args.title, xmin=plot_args.xmin, xmax=plot_args.xmax, ymin=plot_args.ymin, ymax=plot_args.ymax, xlabel=" ".join(plot_args.xlabel) if plot_args.xlabel is not None else None, ylabel=" ".join(plot_args.ylabel) if plot_args.ylabel is not None else None, opacity=plot_args.opacity, + smoothing=plot_args.smoothing, bp_shift=plot_args.bp_shift, combined=plot_args.combined, color_trace=plot_args.color_trace, hide_legend=plot_args.hide_legend) + + # Create arrays for default composite names and colors + names = range(1, len(composite_commands) + 1) + colors = ["#BFBFBF","#000000","#FF0000","#FF9100","#D7D700","#07E200","#00B0F0","#0007FF","#A700FF","#FF00D0"] + # Create parser for composite subcommands + composite_parser = argparse.ArgumentParser() + composite_parser.add_argument("files") + composite_parser.add_argument("--name") + composite_parser.add_argument("--color") + composite_parser.add_argument("--secondary-color") + composite_parser.add_argument("--scale", type=float) + composite_parser.add_argument("--shift-occupancy", type=float) + composite_parser.add_argument("--smoothing", type=float) + composite_parser.add_argument("--opacity", type=float) + composite_parser.add_argument("--bp-shift", type=int) + composite_parser.add_argument("--hide-sense", action="store_true", default=False) + composite_parser.add_argument("--hide-anti", action="store_true", default=False) + composite_parser.add_argument("--swap-strands", action="store_true", default=False) + # Parse composite subcommands, use values values in Composite class if not specified i = 0 - for g in args.composites: - composite_group = CompositeGroup(name=names[i], color=colors[i % len(colors)]) - composite_files = g.split("-") + for command in composite_commands: + args = composite_parser.parse_args(command.split()) + print(args) + composite = Composite(scale=args.scale, color=args.color if args.color is not None else colors[i % len(colors)], secondary_color=args.secondary_color, + smoothing=args.smoothing, bp_shift=args.bp_shift, hide_sense= args.hide_sense, hide_anti= args.hide_anti, baseline=args.shift_occupancy, + name=args.name if args.name is not None else names[i], opacity=args.opacity,) + + composite_files = args.files.split("-") for c in composite_files: #Check if composite file contains multiple composites if sum(1 for line in open(c) if len(line.strip()) != 0) <= 3: - composite = parseComposite.parseComposite(c) - composite_group.loadComposite(composite) + sc = parseComposite.parse_simple(c) + composite.load_simple_composite(sc) else: prefixes = parseComposite.get_prefixes_from_multiple_composites(c) composites = parseComposite.parse_multiple_composite(c, prefixes) - composite_group.loadCompositeDict(composites) - p.add_composite_group(composite_group) - i += 1 - p.autoscale_axes() - group.appendChild(p.plot_composite_groups()) - - generateSVG(p) - with open("out.xml", 'w') as f: - # f.write(template + "\n\t") - group.writexml(f, addindent=' ', newl='\n') + composite.load_composite_dict(composites) + p.add_composite_group(composite) + i += 1 + # If --no-shrink is specified, don't change y-axis but resize x-axis + if plot_args.no_shrink: + p.autoscale_axes(False) + # If --no-resize is specified, don't change either axis + elif not plot_args.no_resize: + p.autoscale_axes(True) + p.plot_composites() + + # Create parser for reference-line subcommand + reference_parser = argparse.ArgumentParser() + reference_parser.add_argument("axis") + reference_parser.add_argument("--style") + reference_parser.add_argument("--color") + reference_parser.add_argument("--val", type=float) + reference_parser.add_argument("--opacity",type=float) + # Add reference lines to plot + for command in ref_line_commands: + args = reference_parser.parse_args(command.split()) + p.plot_reference_line(axis=args.axis, val=args.val, style=args.style, color=args.color, opacity=args.opacity) + # Use svg factory to generate svg based on plot + svg = svgFactory.generateSVG(p) + with open(plot_args.out if plot_args is not None else "out.svg", 'w') as f: + # write to output + svg.writexml(f, addindent=' ', newl='\n') - - print(args.composites) diff --git a/python/slidingWindow.py b/python/slidingWindow.py index 023c5fa..11b900f 100644 --- a/python/slidingWindow.py +++ b/python/slidingWindow.py @@ -1,3 +1,4 @@ +# Copy of sliding_window from plotter def sliding_window(x_domain, occupancy, window): occupancy_val = sum(occupancy[:window]) / window new_xdomain = [(x_domain[0] + x_domain[window - 1]) / 2] From 851025c75404b90f44b9c7849b4b6aba7dd48afe Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Fri, 10 May 2024 20:32:02 -0400 Subject: [PATCH 5/9] fixed bug with loading multicomposites --- python/composite.py | 6 ++++-- python/plot.py | 14 +++++++------- python/plotter.py | 7 ++++--- 3 files changed, 15 insertions(+), 12 deletions(-) diff --git a/python/composite.py b/python/composite.py index f8a37ab..8d5743e 100644 --- a/python/composite.py +++ b/python/composite.py @@ -57,8 +57,9 @@ def load_simple_composite(self,composite: SimpleComposite): j += 1 self.individual_files[composite.id] = composite # Loads dictionary from parse_multiple_composites - def load_composite_dict(self,compositeDict: dict): - for composite in compositeDict: + def load_composite_dict(self,composite_dict: dict): + for key in composite_dict: + composite = composite_dict[key] # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain self.xmin = min(composite.xmin, self.xmin) self.xmax = max(composite.xmax, self.xmax) @@ -74,6 +75,7 @@ def load_composite_dict(self,compositeDict: dict): self.anti = prefix + self.anti + suffix # Update sense and anti arrays j = composite.xmin - self.xmin + print(composite.sense) while j <= composite.xmax - composite.xmin: idx = composite.xmin - self.xmin + j self.sense[idx] += composite.sense[j] diff --git a/python/plot.py b/python/plot.py index 6900d17..6138cd3 100644 --- a/python/plot.py +++ b/python/plot.py @@ -8,7 +8,7 @@ # Class that generates composite and reference lines svg elements class Plot: def __init__(self, title=None, xmin=None, xmax=None, ymin=None, ymax=None, xlabel=None, ylabel=None, - opacity=None, smoothing=None, bp_shift=None, combined=False, color_trace=False, hide_legend=True): + opacity=None, smoothing=None, bp_shift=None, combined=False, color_trace=False, hide_legend=False): # Set variables to defaults if argument passed into constructor was None self.title = title if title is not None else "Composite plot" self.xmin = xmin if xmin is not None else -500 @@ -147,7 +147,7 @@ def plot_composite(self, xmin, xmax, sense, anti, scale=1, color=None, secondary self.plot.appendChild(self.gradients_group) self.plot.appendChild(self.composite_group) - # Creates a composite svg element from a composite_group object, like plotting a row form the settings table + # Creates a composite svg element from a composite object, like plotting a row form the settings table def plot_composite(self, composite): # Set parameters to global values if not specified opacity = composite.opacity if composite.opacity is not None else self.opacity @@ -177,7 +177,7 @@ def plot_composite(self, composite): composite_fill_top = document.createElement("polygon") composite_fill_top.setAttribute("points", " ".join(points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_occupancy[j])}" for j, d in enumerate(truncated_xdomain)]) + f" {self.xscale.get(truncated_xdomain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_xdomain[0])},{self.yscale.get(0)}") composite_fill_top.setAttribute("fill", "url(#composite-gradient-top" + str(i) + ")") - self.composite.appendChild(composite_fill_top) + self.composite_group.appendChild(composite_fill_top) #Create outline wide_trace = document.createElement("path") wide_trace.setAttribute("stroke-width", "1") @@ -334,18 +334,18 @@ def create_legend(self): legend = document.createElement('g') legend.setAttribute("transform", "translate(" + str(self.width - self.margins.get("right") + 25) + " " + str(self.margins.get("top")) + ")") i = 0 - for composite_group in self.composites: + for composite in self.composites: # Creates legend entries for each composite legend_element = document.createElement("g") legend_element.setAttribute("transform", "translate(0," + str(24 * i) + ")") legend_color_sense = document.createElement("polygon") legend_color_sense.setAttribute("points", "0,0 15,0 15,15 0,15") - legend_color_sense.setAttribute("fill", composite_group.color) + legend_color_sense.setAttribute("fill", composite.color) legend_element.appendChild(legend_color_sense) legend_color_anti = document.createElement("polygon") legend_color_anti.setAttribute("points", "0,0 15,0 15,15 0,15") legend_element.appendChild(legend_color_anti) - legend_color_anti.setAttribute("fill", composite_group.secondary_color) + legend_color_anti.setAttribute("fill", composite.secondary_color) legend_border = document.createElement("rect") legend_border.setAttribute("width", "15") legend_border.setAttribute("height", "15") @@ -356,7 +356,7 @@ def create_legend(self): id.setAttribute("x", "20") id.setAttribute("y", "10") id.setAttribute("font-size", "10") - id.appendChild(document.createTextNode(str(composite_group.name))) + id.appendChild(document.createTextNode(str(composite.name))) legend_element.appendChild(id) legend.appendChild(legend_element) i += 1 diff --git a/python/plotter.py b/python/plotter.py index 7978509..ddd88a9 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -58,7 +58,7 @@ def main(): plot_parser.add_argument("--ylabel", nargs="+") plot_parser.add_argument("--color-trace", action="store_true", default=False) plot_parser.add_argument("--combined", action="store_true", default=False) - plot_parser.add_argument("--hide-legend", action="store_false", default=True) + plot_parser.add_argument("--hide-legend", action="store_true", default=False) plot_parser.add_argument("--no-resize", action="store_true", default=False) plot_parser.add_argument("--no-shrink", action="store_true", default=False) plot_parser.add_argument("--reference-line", nargs=3, action='append') @@ -102,8 +102,9 @@ def main(): composite.load_simple_composite(sc) else: prefixes = parseComposite.get_prefixes_from_multiple_composites(c) - composites = parseComposite.parse_multiple_composite(c, prefixes) - composite.load_composite_dict(composites) + print(prefixes) + cd = parseComposite.parse_multiple_composite(c, prefixes[0]) + composite.load_composite_dict(cd) p.add_composite_group(composite) i += 1 # If --no-shrink is specified, don't change y-axis but resize x-axis From e430bc3f3d9f0ab8a00de78bf6af6ae7288d50c1 Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Sat, 11 May 2024 18:07:31 -0400 Subject: [PATCH 6/9] Added readme and import/export json --- .gitignore | 6 +- python/__pycache__/composite.cpython-312.pyc | Bin 0 -> 5967 bytes .../parseComposite.cpython-312.pyc | Bin 0 -> 7186 bytes .../__pycache__/parseComposite.cpython-39.pyc | Bin 0 -> 4217 bytes python/__pycache__/plot.cpython-312.pyc | Bin 0 -> 44918 bytes .../__pycache__/slidingWindow.cpython-312.pyc | Bin 0 -> 962 bytes python/__pycache__/svgFactory.cpython-312.pyc | Bin 0 -> 14553 bytes python/composite.py | 13 +- python/out.svg | 123 ++++++++++ python/parseComposite.py | 144 ++++++++++++ python/plot.py | 64 +++++- python/plotter.py | 33 ++- python/readme.md | 94 ++++++++ python/slidingWindow.py | 8 +- python/svgFactory.py | 215 ++++++++++++++++++ 15 files changed, 678 insertions(+), 22 deletions(-) create mode 100644 python/__pycache__/composite.cpython-312.pyc create mode 100644 python/__pycache__/parseComposite.cpython-312.pyc create mode 100644 python/__pycache__/parseComposite.cpython-39.pyc create mode 100644 python/__pycache__/plot.cpython-312.pyc create mode 100644 python/__pycache__/slidingWindow.cpython-312.pyc create mode 100644 python/__pycache__/svgFactory.cpython-312.pyc create mode 100644 python/out.svg create mode 100644 python/parseComposite.py create mode 100644 python/readme.md create mode 100644 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hide_anti=False, baseline=0, name=None, sense=None, anti=None, xmin=None, xmax=None): # Sets default values self.scale = scale if scale is not None else 1 self.color = color if color is not None else "#0000FF" self.secondary_color = secondary_color if secondary_color is not None else color self.baseline = baseline if baseline is not None else 0 - self.xmin = 0 - self.xmax = 0 - self.sense = [] - self.anti = [] + self.xmin = xmin if xmin is not None else 0 + self.xmax = xmax if xmax is not None else 0 + self.sense = sense if sense is not None else [] + self.anti = anti if anti is not None else [] + # Don't assign defaults to opacity, smoothing, and bp_shift so plot can apply plot defaults self.opacity = opacity self.smoothing = smoothing self.bp_shift = bp_shift @@ -75,12 +76,12 @@ def load_composite_dict(self,composite_dict: dict): self.anti = prefix + self.anti + suffix # Update sense and anti arrays j = composite.xmin - self.xmin - print(composite.sense) while j <= composite.xmax - composite.xmin: idx = composite.xmin - self.xmin + j self.sense[idx] += composite.sense[j] self.anti[idx] += composite.anti[j] j += 1 self.individual_files[composite.id] = composite + def __str__(self): return str(self.individual_files) \ No newline at end of file diff --git a/python/out.svg b/python/out.svg new file mode 100644 index 0000000..3831ed0 --- /dev/null +++ b/python/out.svg @@ -0,0 +1,123 @@ + + -4.6 + + Only the biggest PLOT + Position (bp) + + okay X10 + -1 + + -549 + 550 + 4.7 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + 1_imported + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/python/parseComposite.py b/python/parseComposite.py new file mode 100644 index 0000000..ccbaaf3 --- /dev/null +++ b/python/parseComposite.py @@ -0,0 +1,144 @@ +import csv +import xml.dom.minidom as dom +import argparse +import math +import composite +import os + +# Returns a simple composite from a single file +def parse_simple(file): + fileArr = open(file, "r").read().split("\n") + xmin = None + xmax = None + sense = [] + anti = [] + xmin_curr = 0 + xmax_curr = 0 + offset = 0 + for line in fileArr: + # Skip empty + if len(line.strip()) == 0 : + continue + # Separate fields + fields = line.split("\t") + if not fields[0].strip() or fields[0] == "NAME": + xmin_curr = int(float(fields[1])) + xmax_curr = int(float(fields[-1])) + # If the x domain starts at 0 shift it to the left + if xmin_curr == 0: + xmin_curr -= math.floor(xmax_curr / 2) + xmax_curr -= math.floor(xmax_curr / 2) + # If the x domain is not defined yet, define it + if xmin == None or xmax == None: + xmin = xmin_curr + xmax = xmax_curr + # Redefine min and max if necessary + xmax = max(xmax_curr, xmax) + xmin = min(xmin_curr, xmin) + sense = [0] * (xmax - xmin + 1) + anti = [0] * (xmax - xmin + 1) + # Add the values to sense and anti arrays + if "sense" in fields[0].lower(): + i = 1 + while i < len(fields): + sense[offset + i - 1] += float(fields[i]) + i += 1 + elif "anti" in fields[0].lower(): + i = 1 + while i < len(fields): + anti[offset + i - 1] += float(fields[i]) + i += 1 + # If the first field is not empty or "NAME" and does not contain "sense" or "anti" parse as combined or midpoint data + elif not (fields[0] == "" or fields[0] == "NAME"): + i = 1 + while i < len(fields): + sense[offset + i - 1] += float(fields[i]) / 2 + anti[offset + i - 1] += float(fields[i]) / 2 + return composite.SimpleComposite(xmin, xmax, sense, anti, os.path.basename(file).split('_')[0]) + +# Returns list of prefixes from multi-composite file, mimics the plotter method +def get_prefixes_from_multiple_composites(file): + lines = open(file, "r").read().split("\n") + names_list = [] + i = 0 + while i < len(lines): + line = lines[i] + # Skip empty + if line.strip() == "": + i += 1 + continue + # Get the first field + col0 = line.split("\t")[0] + if col0 == "" or col0[0] == "NAME": + # Get the names of the composites for lines immediately following the xdomain + i += 1 + names_list.append(lines[i].split("\t")[0]) + i += 1 + # Take the first name and split it by "_" + split_name = names_list[0].split("_") + idx = None + # Iterate over each possible prefix-suffix split + for i in range(1, len(split_name) - 1): + prefix = "_".join(split_name[:i]) + suffix = "_".join(split_name[i:]) + n_prefix = sum(1 for n in names_list if n.startswith(prefix)) + n_suffix = sum(1 for n in names_list if n.endswith(suffix)) + if n_prefix * n_suffix == len(names_list): + if n_suffix == len(names_list): + idx = i if idx is None else idx + break + idx = i + suffix = "_".join(split_name[idx:]) + # Get the prefixes by removing the suffix from the names + return [n[:-len(suffix)] for n in names_list if n.endswith(suffix)] + +# Returns dictionary with composite from multi-composite file, mimics the plotter method +def parse_multiple_composite(file, prefix): + lines = open(file, "r").read().split("\n") + composites = {} + xmin = None + xmax = None + sense = [] + anti = [] + i = 0 + id = 0 + save_comp = False + while i < len(lines): + line = lines[i] + # Skip empty + if line.strip() == "": + i += 1 + continue + # Get the first field + fields = line.split("\t") + col0 = fields[0] + if not col0.strip() or col0 == "NAME": + # If the x domain is defined, save the composite + if save_comp: + composites[id] = composite.SimpleComposite(xmin, xmax, sense, anti, id) + save_comp = False + # Get the nex x domain + fields = [field for field in fields if field.strip()] + xmin = int(float(fields[0])) + xmax = int(float(fields[-1])) + # If the x domain starts at 0 shift it to the left + if xmin == 0: + xmin -= math.floor(xmax / 2) + xmin -= math.floor(xmax / 2) + elif col0.startswith(prefix): + id = col0[len(prefix):].split("_")[0] + save_comp = True + # Add the values to sense and anti arrays + fields = [field for field in fields if field.strip()] + if "sense" in fields[0].lower(): + sense = [float(val) for val in fields[1:]] + elif "anti" in fields[0].lower(): + anti = [float(val) for val in fields[1:]] + else: + sense = [float(val) / 2 for val in fields[1:]] + anti = [float(val) / 2 for val in fields[1:]] + i += 1 + # Save the last composite + if save_comp: + composites[id] = composite.SimpleComposite(xmin, xmax, sense, anti, id) + return composites \ No newline at end of file diff --git a/python/plot.py b/python/plot.py index 6138cd3..fd9832e 100644 --- a/python/plot.py +++ b/python/plot.py @@ -2,6 +2,8 @@ import copy import slidingWindow import math +import json +import composite document = dom.Document() @@ -205,7 +207,7 @@ def plot_composite(self, composite): scaled_anti = [value if (value := d * composite.scale + composite.baseline) > 0 else 0 for j, d in enumerate(smoothed_anti) if int(new_xdomain[j] - bp_shift) >= self.xmin and int(new_xdomain[j] - bp_shift) <= self.xmax] # Create sense trace and polygon if not hidden - if not composite.hide_anti: + if not composite.hide_sense: # Create top polygon composite_fill_top = document.createElement("polygon") composite_fill_top.setAttribute("points", " ".join(sense_points := [f"{self.xscale.get(d)},{self.yscale.get(scaled_sense[j])}" for j, d in enumerate(truncated_sense_domain)]) + f" {self.xscale.get(truncated_sense_domain[-1])},{self.yscale.get(0)} {self.xscale.get(truncated_sense_domain[0])},{self.yscale.get(0)}") @@ -365,6 +367,64 @@ def create_legend(self): # Returns svg group with all composites and reference lines def get_plot(self): return self.plot + + # Exports json of all composites and plot attributes + def export(self): + composite_arr = [] + for composite in self.composites: + composite_arr.append({ + 'name': composite.name, + 'xmin': composite.xmin, + 'xmax': composite.xmax, + 'sense': composite.sense, + 'anti': composite.anti, + 'color': composite.color, + 'secondary-color': composite.secondary_color, + 'scale': composite.scale, + 'opacity': composite.opacity, + 'smoothing': composite.smoothing, + 'bp_shift': composite.bp_shift, + 'hide_sense': composite.hide_sense, + 'hide_anti': composite.hide_anti, + 'files_loaded': composite.files_loaded + }) + return { + 'settings' :composite_arr, + 'plot' : {'title': self.title, 'xlabel': self.xlabel, 'ylabel': self.ylabel, 'opacity': self.opacity, + 'smoothing': self.smoothing, 'bp_shift': self.bp_shift, 'xmin': self.xmin, 'xmax': self.xmax, 'ymin': self.ymin, + 'ymax': self.ymax, 'combined': self.combined, 'color_trace': self.color_trace, 'hide_legend': self.hide_legend} + } + + # Imports JSON with plot attributes and composites if desired. Preserves plot options specified by most recent call + def import_data(self, file, args, import_composites): + with open(file) as f: + data = json.load(f) + if import_composites: + for c in data['settings']: + n = c.get('name') + # Add _imported to composite name if duplicate of existing composite + if any(n == self.composites[j].name for j in range(len(self.composites))): + n = str(n) + "_imported" + self.composites.append(composite.Composite(scale=c.get('scale'), color=c.get('color'), secondary_color=c.get('secondary-color'), opacity=c.get('opacity'), + smoothing=c.get('smoothing'), bp_shift=c.get('bp_shift'), hide_sense=c.get('hide_sense'), hide_anti=c.get('hide_anti'), + baseline=c.get('baseline'), name=n, sense=c.get('sense'), anti=c.get('anti'), xmin=c.get('xmin'), xmax=c.get('xmax'))) + plot_data = data['plot'] + # Add plot variables + self.title = plot_data.get('title', self.title) if args.title is None else self.title + self.xmin = plot_data.get('xmin', self.xmin) if args.xmin is None else self.xmin + self.xmax = plot_data.get('xmax', self.xmax) if args.xmax is None else self.xmax + self.ymin = plot_data.get('ymin', self.ymin) if args.ymin is None else self.ymin + self.ymax = plot_data.get('ymax', self.ymax) if args.ymax is None else self.ymax + self.xlabel = plot_data.get('xlabel', self.xlabel) if args.xlabel is None else self.xlabel + self.ylabel = plot_data.get('ylabel', self.ylabel) if args.ylabel is None else self.ylabel + self.opacity = plot_data.get('opacity', self.opacity) if args.opacity is None else self.opacity + self.smoothing = plot_data.get('smoothing', self.smoothing) if args.smoothing is None else self.smoothing + self.bp_shift = plot_data.get('bp_shift', self.bp_shift) if args.bp_shift is None else self.bp_shift + self.combined = plot_data.get('combined', self.combined) if args.combined is None else self.combined + self.color_trace = plot_data.get('color_trace', self.color_trace) if args.color_trace is None else self.color_trace + self.hide_legend = plot_data.get('hide_legend', self.hide_legend) if args.hide_legend is None else self.hide_legend + self.xscale = XScale(self) + self.yscale = YScale(self) def generateGradients(self, opacity, i, color, secondary_color=None): # Creates DOM elements for top and bottom gradients @@ -406,8 +466,8 @@ def generateGradients(self, opacity, i, color, secondary_color=None): bottom_stop_two.setAttribute("stop-opacity", "0") composite_gradient_bottom.appendChild(bottom_stop_one) composite_gradient_bottom.appendChild(bottom_stop_two) - self.gradients_group.appendChild(composite_gradient_bottom) + # Class that mimics d3 scaleLinear() for x-axis of plot class XScale: def __init__(self, plot): diff --git a/python/plotter.py b/python/plotter.py index ddd88a9..5515b1b 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -10,6 +10,7 @@ import sys from enum import Enum import svgFactory +import json document = dom.Document() @@ -25,9 +26,8 @@ def main(): composite_commands = [] ref_line_commands = [] plot_command = "" - current = "composite" + current = "" for word in sys.argv: - print(word) if word == "composite": i += 1 composite_commands.append("") @@ -49,7 +49,7 @@ def main(): plot_parser.add_argument("--smoothing", type=float) plot_parser.add_argument("--bp-shift", type=int) plot_parser.add_argument("--opacity", type=float) - plot_parser.add_argument("--title") + plot_parser.add_argument("--title", nargs="+") plot_parser.add_argument("--xmin",type=int) plot_parser.add_argument("--xmax",type=int) plot_parser.add_argument("--xlabel", nargs="+") @@ -61,11 +61,14 @@ def main(): plot_parser.add_argument("--hide-legend", action="store_true", default=False) plot_parser.add_argument("--no-resize", action="store_true", default=False) plot_parser.add_argument("--no-shrink", action="store_true", default=False) - plot_parser.add_argument("--reference-line", nargs=3, action='append') plot_parser.add_argument("--out") + plot_parser.add_argument("--export-json") + plot_parser.add_argument("--import-json") + plot_parser.add_argument("--import-settings-json") + # Create plot based on plot subcommand, default values in Plot class will be used if argument is not specified plot_args = plot_parser.parse_args(plot_command.split()) - p = plot.Plot(title=plot_args.title, xmin=plot_args.xmin, xmax=plot_args.xmax, ymin=plot_args.ymin, ymax=plot_args.ymax, xlabel=" ".join(plot_args.xlabel) if plot_args.xlabel is not None else None, ylabel=" ".join(plot_args.ylabel) if plot_args.ylabel is not None else None, opacity=plot_args.opacity, + p = plot.Plot(title=" ".join(plot_args.title), xmin=plot_args.xmin, xmax=plot_args.xmax, ymin=plot_args.ymin, ymax=plot_args.ymax, xlabel=" ".join(plot_args.xlabel) if plot_args.xlabel is not None else None, ylabel=" ".join(plot_args.ylabel) if plot_args.ylabel is not None else None, opacity=plot_args.opacity, smoothing=plot_args.smoothing, bp_shift=plot_args.bp_shift, combined=plot_args.combined, color_trace=plot_args.color_trace, hide_legend=plot_args.hide_legend) # Create arrays for default composite names and colors @@ -89,7 +92,6 @@ def main(): i = 0 for command in composite_commands: args = composite_parser.parse_args(command.split()) - print(args) composite = Composite(scale=args.scale, color=args.color if args.color is not None else colors[i % len(colors)], secondary_color=args.secondary_color, smoothing=args.smoothing, bp_shift=args.bp_shift, hide_sense= args.hide_sense, hide_anti= args.hide_anti, baseline=args.shift_occupancy, name=args.name if args.name is not None else names[i], opacity=args.opacity,) @@ -102,17 +104,24 @@ def main(): composite.load_simple_composite(sc) else: prefixes = parseComposite.get_prefixes_from_multiple_composites(c) - print(prefixes) cd = parseComposite.parse_multiple_composite(c, prefixes[0]) composite.load_composite_dict(cd) p.add_composite_group(composite) i += 1 + + # Import settings and composites from plot, preserving options specified in this call + if plot_args.import_json: + p.import_data(plot_args.import_json, plot_args, True) + elif plot_args.import_settings_json: + p.import_data(plot_args.import_settings_json, plot_args, False) + # If --no-shrink is specified, don't change y-axis but resize x-axis if plot_args.no_shrink: p.autoscale_axes(False) # If --no-resize is specified, don't change either axis elif not plot_args.no_resize: p.autoscale_axes(True) + p.plot_composites() # Create parser for reference-line subcommand @@ -128,7 +137,13 @@ def main(): p.plot_reference_line(axis=args.axis, val=args.val, style=args.style, color=args.color, opacity=args.opacity) # Use svg factory to generate svg based on plot svg = svgFactory.generateSVG(p) - with open(plot_args.out if plot_args is not None else "out.svg", 'w') as f: + with open(plot_args.out if plot_args.out is not None else "out.svg", 'w') as f: # write to output svg.writexml(f, addindent=' ', newl='\n') - + + # Output plot json if specified + if plot_args.export_json: + str = json.dumps(p.export(), indent=2) + with open(plot_args.export_json, 'w') as f: + # Write to output + f.write(str) \ No newline at end of file diff --git a/python/readme.md b/python/readme.md new file mode 100644 index 0000000..ed279a9 --- /dev/null +++ b/python/readme.md @@ -0,0 +1,94 @@ +## Python Plotter + +This is a Python implementation of a plotter that creates plot-esque plots based on subcommands passed into `plotter.py`. + +The three basic subcommands are `composite`, `plot`, and `reference-line`. They're passed into `plotter.py` using a single line with the basic syntax: + +``` +python plotter.py composite [file] [composite options] reference-line [axis] [line options] plot [plot options] +``` + +An example command is: + +``` +python plotter.py composite sample.out --bp-shift 50 composite sample2.out --bp-shift 50 reference-line y --color blue plot --title "Samples One and Two" --smoothing 10 --out out.svg +``` + +The `composite` and `reference-line` subcommands can be repeated for as many composites or reference lines as you wish to add, but the `plot` command should only be used once per call. If `--opacity`, `--smoothing`, or `--bp-shift` is specified for a composite, those specifications will override default values inherited by values specified in the plot subcommand. Also, all boolean options are flags; if not specified they will remain the default value. + +### Plot + +``` +plot [plot options] +``` + +The `plot` subcommand takes no positional arguments, and the options specify properties for the entire plot, such as domain, range, and the axis labels. Options can also be used to specify default properties for all composites such as `opacity` and `smoothing`. This implementation of the plotter autoscales the axes to fit the largest composite by default, ignoring the `xmin`, `xmax`, `ymin`, and `ymax` options unless `--no-shirk` or `--no-resize` is specified. + +The available options for the `plot` subcommand are: + +| Command | Type | Description | Default | +| ---------------- | ------- | ---------------------------------------- | --------------- | +| --smoothing | Float | The default smoothing value | 7 | +| --bp-shift | Int | The default bp-shift | 0 | +| --opacity | Float | The default maximum opacity | 1 | +| --title | String | The title of the plot | "Composite plot" | +| --xmin | Int | Minimum value of the plot | -500 | +| --xmax | Int | Maximum value of the plot | 500 | +| --ymin | Int | Minimum occupancy of the plot | -1 | +| --ymax | Int | Maximum occupancy of the plot | 1 | +| --ylabel | String | Label for the y-axis | Occupancy (AU) | +| --xlabel | String | Label for the x-axis | Position (bp) | +| --color-trace | Boolean | Default for if composites should have composite trace | False | +| --combined | Boolean | Draws a combined plot | False | +| --hide-legend | Boolean | Hides the plot legend | False | +| --no-resize | Boolean | Prevents plotter from autoscaling the x and y axes | False | +| --no-shrink | Boolean | Prevents plotter from autoscaling the y-axis | False | +| --out | String | Name and filepath of svg output | `out.svg` | +| --export-json | String | JSON file to export composites and plot settings | `None` | +| --import-json | String | JSON file to import composites and plot settings | `None` | +| --import-settings-json | String | JSON file to import plot settings | `None` | + +### Composite + +``` +composite [file] [composite options] +``` + +The `composite` subcommand takes a positional argument that specifies the files to be loaded into the composite. If there are multiple files, they should be separated by a "-". For example, `composite sample1.out-sample2.out-sample3.out --opacity 0.5` loads samples 1-3 into the composite and sets the maximum opacity to 0.5. + +The available options for the `composite` subcommand are: + +| Command | Type | Description | Default | +| ----------------- | ------- | ---------------------------------------- | --------------- | +| --name | String | Assigns the name of the composite for the plot's legend | None | +| --color | String | Sets the color of the composite using hex code or default HTML color | Plotter Defaults | +| --secondary-color | String | Sets the secondary color of the composite using hex code or default HTML color | The primary color | +| --scale | Float | Sets the scale of the composite | 1 | +| --shift-occupancy | Float | Shifts occupancy by a set value | 0 | +| --smoothing | Float | Sets smoothing | 7 | +| --opacity | Float | Sets opacity | 1 | +| --bp-shift | Int | Sets bp shift | 0 | +| --hide-sense | Boolean | Hides the sense strand | False | +| --hide-anti | Boolean | Hides the anti strand | False | +| --swap-strands | Boolean | Swaps the sense and anti strands | False | +| --export-json | String | Path to export json with composites and plot values| None | +| --import-json | String | Path to import json with composites and plot values | None | + +### Reference-Line + +``` +reference-line [axis] [reference-line options] +``` + +The `reference-line` subcommand takes either `x` or `y` to specify the axis it should be plotted on followed by options specifying its attributes. + +The available options for the `reference-line` subcommand are: + +| Command | Type | Description | Default | +| ---------------- | ------- | ---------------------------------------- | --------------- | +| --val | Float | Sets the position of the line (bp if x-axis or AU if y-axis) | 0 | +| --color | String | Sets the color of the line using hex code or default HTML color | Plotter Defaults | +| --style | `dashed`, `dotted`, or `solid` | Sets the style of the line | `dashed` | +| --opacity | Float | Sets the opacity | 1 | + +--- \ No newline at end of file diff --git a/python/slidingWindow.py b/python/slidingWindow.py index 11b900f..0a5781b 100644 --- a/python/slidingWindow.py +++ b/python/slidingWindow.py @@ -1,10 +1,12 @@ # Copy of sliding_window from plotter -def sliding_window(x_domain, occupancy, window): +def sliding_window(xdomain, occupancy, window): occupancy_val = sum(occupancy[:window]) / window - new_xdomain = [(x_domain[0] + x_domain[window - 1]) / 2] + print("length: " + str(xdomain)) + + new_xdomain = [(xdomain[0] + xdomain[window - 1]) / 2] new_occupancy = [occupancy_val] for i in range(len(occupancy) - window - 1): - new_xdomain.append((x_domain[i + 1] + x_domain[i + window]) / 2) # Added parentheses here + new_xdomain.append((xdomain[i + 1] + xdomain[i + window]) / 2) # Added parentheses here occupancy_val += (occupancy[i + window] - occupancy[i]) / window new_occupancy.append(occupancy_val) return {"new_xdomain": new_xdomain, "new_occupancy": new_occupancy} \ No newline at end of file diff --git a/python/svgFactory.py b/python/svgFactory.py new file mode 100644 index 0000000..7003376 --- /dev/null +++ b/python/svgFactory.py @@ -0,0 +1,215 @@ +import plot +import composite +from composite import Composite +from composite import SimpleComposite +import re +import xml.dom.minidom as dom +import argparse +import math +import parseComposite +import sys +from enum import Enum + +document = dom.Document() + +def generateSVG(plot): + # Create svg with similar attributes to plotter + svg = document.appendChild(document.createElement('svg')) + svg.setAttribute("xmlns", "http://www.w3.org/2000/svg") + svg.setAttribute("id", "main-plot") + svg.setAttribute("font-family", "Helvetica") + svg.setAttribute("viewBox", "0 0 460 300") + svg.setAttribute("style", "height: 50vh; max-width: 100%; overflow: hide;") + svg.setAttribute("baseProfile", "full") + # Create title + title = document.createElement('text') + title.setAttribute("font-size", "16") + title.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) + title.setAttribute("y", "20") + title.setAttribute("label", "title") + title.setAttribute("id", "main-plot-title") + title.setAttribute("style", "text-anchor: middle; cursor: pointer;") + title.appendChild(document.createTextNode(plot.title)) + # Create xlabel, xmin and xmax + xlabel = document.createElement('text') + xlabel.setAttribute("font-size", "16") + xlabel.setAttribute("x", str((plot.width + plot.margins.get('left') - plot.margins.get('right')) / 2)) + xlabel.setAttribute("y", str(plot.height - 5)) + xlabel.setAttribute("label", "xlabel") + xlabel.setAttribute("id", "main-plot-xlabel") + xlabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") + xlabel.appendChild(document.createTextNode(plot.xlabel)) + xmin = document.createElement('text') + xmin.setAttribute("x", str(plot.margins.get("left"))) + xmin.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) + xmin.setAttribute("text-anchor", "middle") + xmin.setAttribute("font-size", "14px") + xmin.appendChild(document.createTextNode(str(plot.xmin))) + xmax = document.createElement('text') + xmax.setAttribute("x", str(plot.width - plot.margins.get("right"))) + xmax.setAttribute("y", str(plot.height - plot.margins.get("bottom") + 15)) + xmax.setAttribute("text-anchor", "middle") + xmax.setAttribute("font-size", "14px") + xmax.appendChild(document.createTextNode(str(plot.xmax))) + # Create ylabel with exponent + ylabel = document.createElement('text') + ylabel.setAttribute("font-size", "16") + ylabel.setAttribute("x", "12") + ylabel.setAttribute("y", str((plot.height + plot.margins.get('top') - plot.margins.get('bottom')) / 2)) + ylabel.setAttribute("label", "ylabel") + ylabel.setAttribute("id", "main-plot-ylabel") + ylabel.setAttribute("transform", "rotate(-90 12 147.5)") + ylabel.setAttribute("style", "text-anchor: middle; cursor: pointer;") + round_exp = 1 - math.floor(math.log10(plot.ymax - plot.ymin)) + round_factor = 10 ** round_exp + exp_label = round_exp <= -2 or round_exp >= 2 + if exp_label: + ylabel.appendChild(document.createTextNode(plot.ylabel + " X10")) + ylabel_suffix = document.createElement("tspan") + ylabel_suffix.setAttribute("font-size", "8px") + ylabel_suffix.setAttribute("baseline-shift", "super") + ylabel_suffix.appendChild(document.createTextNode(str(1 - round_exp))) + ylabel.appendChild(ylabel_suffix) + else: + ylabel.appendChild(document.createTextNode(plot.ylabel)) + # Create ymin and ymax + if not plot.combined: + ymin = document.createElement('text') + ymin.setAttribute("x", "30") + ymin.setAttribute("y", str(plot.height - plot.margins.get("bottom"))) + ymin.setAttribute("text-anchor", "end") + ymin.setAttribute("font-size", "14px") + ymin.appendChild(document.createTextNode(str((round(plot.ymin, 2) * round_factor) / (10 if exp_label else round_factor)))) + svg.appendChild(ymin) + ymax = document.createElement('text') + ymax.setAttribute("x", "30") + ymax.setAttribute("y", str(plot.margins.get("top") + 10)) + ymax.setAttribute("text-anchor", "end") + ymax.setAttribute("font-size", "14px") + ymax.appendChild(document.createTextNode(str((round(plot.ymax, 2) * round_factor) / (10 if exp_label else round_factor)))) + # Create vertical line at reference point + zero_line = document.createElement("line") + zero_line.setAttribute("stroke", "grey") + zero_line.setAttribute("opacity", "0.5") + zero_line.setAttribute("y1", str(plot.margins.get("top"))) + zero_line.setAttribute("y2", str(plot.height - plot.margins.get("bottom"))) + zero_line.setAttribute("x1", str(plot.xscale.get(0))) + zero_line.setAttribute("x2", str(plot.xscale.get(0))) + zero_line.setAttribute("stroke-dasharray", "5,5") + svg.appendChild(zero_line) + svg.appendChild(title) + svg.appendChild(xlabel) + svg.appendChild(ylabel) + svg.appendChild(xmin) + svg.appendChild(xmax) + svg.appendChild(ymax) + # Append composites, reference lines, and legend from plot onto svg + plot.create_legend() + svg.appendChild(plot.get_plot()) + # Create axes with tick marks + axis_left = axis("left", None, plot) + axis_right = axis("right", None, plot) + axis_bottom = axis("bottom", None, plot) + axis_top = axis("top", None, plot) + axis_middle = axis("middle", None, plot) + # Append all elements to svg + svg.appendChild(axis_left) + svg.appendChild(axis_right) + svg.appendChild(axis_bottom) + svg.appendChild(axis_top) + svg.appendChild(axis_middle) + # Return the svg + return svg + +# Create axis elements for plot +def axis(orient, scale, plot): + # Use appropriate tick parameters for axis + tickSpacing = 23.5 if orient == "left" or orient == "right" else 25 + tickSize = 6 if orient == "left" or orient == "top" else -6 + axis_group = document.createElement("g") + axis = document.createElement("line") + # Get coords for plot margins + bottom = plot.height - plot.margins.get('bottom') + top = plot.margins.get("top") + right = plot.width - (plot.margins.get('right')) + left = plot.margins.get("left") + match orient: + # Draw left axis + case "left": + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(left)) + axis.setAttribute("y1", str(top)) + axis.setAttribute("y2", str(bottom)) + i = top + while i < bottom: + tick = document.createElement("line") + tick.setAttribute("y1", str(i)) + tick.setAttribute("y2", str(i)) + tick.setAttribute("x1", str(left)) + tick.setAttribute("x2", str(left + tickSize)) + axis_group.appendChild(tick) + i += tickSpacing + # Draw right axis + case "right": + axis.setAttribute("x1", str(right)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(top)) + axis.setAttribute("y2", str(bottom)) + i = top + while i < bottom: + tick = document.createElement("line") + tick.setAttribute("y1", str(i)) + tick.setAttribute("y2", str(i)) + tick.setAttribute("x1", str(right)) + tick.setAttribute("x2", str(right + tickSize)) + axis_group.appendChild(tick) + i += tickSpacing + # Draw bottom axis + case "bottom": + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(bottom)) + axis.setAttribute("y2", str(bottom)) + i = left + while i < right: + tick = document.createElement("line") + tick.setAttribute("y1", str(bottom)) + tick.setAttribute("y2", str(bottom + tickSize)) + tick.setAttribute("x1", str(i)) + tick.setAttribute("x2", str(i)) + axis_group.appendChild(tick) + i += tickSpacing + # Draw top axis + case "top": + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(top)) + axis.setAttribute("y2", str(top)) + i = left + while i < right: + tick = document.createElement("line") + tick.setAttribute("y1", str(top)) + tick.setAttribute("y2", str(top + tickSize)) + tick.setAttribute("x1", str(i)) + tick.setAttribute("x2", str(i)) + axis_group.appendChild(tick) + i += tickSpacing + # Draw middle axis if plot is not combined + case "middle": + if not plot.combined == True: + axis.setAttribute("x1", str(left)) + axis.setAttribute("x2", str(right)) + axis.setAttribute("y1", str(plot.yscale.get(0))) + axis.setAttribute("y2", str(plot.yscale.get(0))) + i = left + while i < right: + tick = document.createElement("line") + tick.setAttribute("y1", str(plot.yscale.get(0) - tickSize)) + tick.setAttribute("y2", str(plot.yscale.get(0) + tickSize)) + tick.setAttribute("x1", str(i)) + tick.setAttribute("x2", str(i)) + axis_group.appendChild(tick) + i += tickSpacing + axis_group.setAttribute("stroke", "black") + axis_group.appendChild(axis) + return axis_group \ No newline at end of file From ab8d4425430003c1031a1b67e80cc2a082b434d8 Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Fri, 17 May 2024 12:37:37 -0400 Subject: [PATCH 7/9] Changed match to if statements and fixed readme typo --- python/__pycache__/composite.cpython-312.pyc | Bin 5967 -> 5967 bytes python/__pycache__/plot.cpython-312.pyc | Bin 44918 -> 44918 bytes python/__pycache__/svgFactory.cpython-312.pyc | Bin 14553 -> 14564 bytes python/plotter.py | 4 +- python/readme.md | 2 +- python/svgFactory.py | 135 +++++++++--------- 6 files changed, 70 insertions(+), 71 deletions(-) diff --git a/python/__pycache__/composite.cpython-312.pyc b/python/__pycache__/composite.cpython-312.pyc index f4942a99a1a2163a8a01d7116a042741be66be73..097686efa07ca265aaf0f0de90dea282123ff3d2 100644 GIT binary patch delta 75 zcmX@FcV3V8G%qg~0}w2IZJ%~-BkxC6#s{1Kv;JgdRNMTMyOf>Lc5}XPEfZtdz btU|1kA2cR6itXojV`S9&!~i0T1c15$>8%&2 delta 75 zcmX@FcV3V8G%qg~0}xmpwol92$or9%@y6!=tUp;9RX6|SE@fx5*_#;1zjH}SUPpoO^UD%a0W$)z}%tur>pg~&+ zx)kV2hgB$Okd_<@>`X=X7=mFX@9NxMD`7b%O<>AVKhs!-Qc3^engLHd{a-+}*$sJq zhFr;(0;vcQ%nzt=@F+kOD@Cxm0mvvIBgpFP`@-d$Yd~xzA`oT!iZFor zK@|=e!5C`?1>{+stpqf-(o>&>5zeF$k3m4`ss<0hQF`68**iHa=KEC`F`m43C-+5o zB$^AD>eLwS>GI>{vPe=6h{uJ`B-=5Q*;g VIh&9uzwK`a=Ia317O(2>-EYaU!4m)g delta 984 zcmbVKOH30{6zxNP{Xd!47A=-fnRb{K+EVDKFcbtDHb5jM65SROlnv-YBhjtKXa=uD zT(!{+Sd2ruV8OyJjES`Q+T(Pjm0*99wp~ z#YAhRker@k*BuRh^erFqXOQh0N~6o1$t0n95A+9*!8UJ$Oeg{E?0s|xe34Q3%JcBD z!v@Jf!TyEfD-Pi!!B=SZ05$=UAc3EJ3w-3x+22y0fQE=0x#A=q>N>NHn+>7GEPe(LcJLT?I zY#hwhYB*+89F)1$F_r7laPOXA&r;hDD(Kc3&m(bB%nqpxXC(b;_2s2NL};j1xuk~s zOW#}NuTJVEq`N)K?1PyPUVqUWQ@k-bpn6Y9Lv&UotU}mqdTmgy+_0`&H=OIv0#c)A z3X@87R1J@5Wc Date: Mon, 17 Jun 2024 13:21:42 -0400 Subject: [PATCH 8/9] hotfix for smoothing --- python/plotter.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/plotter.py b/python/plotter.py index d6e14d0..45a63e6 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -46,7 +46,7 @@ def main(): plot_command += f" {word}" # Create parser for plot subcommand plot_parser = argparse.ArgumentParser() - plot_parser.add_argument("--smoothing", type=float) + plot_parser.add_argument("--smoothing", type=int) plot_parser.add_argument("--bp-shift", type=int) plot_parser.add_argument("--opacity", type=float) plot_parser.add_argument("--title", nargs="+") @@ -82,7 +82,7 @@ def main(): composite_parser.add_argument("--secondary-color") composite_parser.add_argument("--scale", type=float) composite_parser.add_argument("--shift-occupancy", type=float) - composite_parser.add_argument("--smoothing", type=float) + composite_parser.add_argument("--smoothing", type=int) composite_parser.add_argument("--opacity", type=float) composite_parser.add_argument("--bp-shift", type=int) composite_parser.add_argument("--hide-sense", action="store_true", default=False) From 703d445b563d0b62f1e1f57a42f9f2cd14616276 Mon Sep 17 00:00:00 2001 From: benjaminbeer256 <95663373+benjaminbeer256@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:31:21 -0400 Subject: [PATCH 9/9] changed file separator to colon and removed log statements + pycache --- .gitignore | 1 + js/events/load_composite_button.js | 1 - js/parse_composite.js | 3 --- js/widgets/main_plot.js | 3 --- python/__pycache__/composite.cpython-312.pyc | Bin 5967 -> 0 bytes python/__pycache__/composite.cpython-39.pyc | Bin 3464 -> 0 bytes .../__pycache__/parseComposite.cpython-312.pyc | Bin 7186 -> 0 bytes .../__pycache__/parseComposite.cpython-39.pyc | Bin 4217 -> 0 bytes python/__pycache__/plot.cpython-312.pyc | Bin 44918 -> 0 bytes python/__pycache__/plot.cpython-39.pyc | Bin 8838 -> 0 bytes .../__pycache__/slidingWindow.cpython-312.pyc | Bin 962 -> 0 bytes .../__pycache__/slidingWindow.cpython-39.pyc | Bin 545 -> 0 bytes python/__pycache__/svgFactory.cpython-312.pyc | Bin 14564 -> 0 bytes python/plot.py | 17 ++++++++++++++--- python/plotter.py | 2 +- python/readme.md | 2 +- python/slidingWindow.py | 1 - 17 files changed, 17 insertions(+), 13 deletions(-) delete mode 100644 python/__pycache__/composite.cpython-312.pyc delete mode 100644 python/__pycache__/composite.cpython-39.pyc delete mode 100644 python/__pycache__/parseComposite.cpython-312.pyc delete mode 100644 python/__pycache__/parseComposite.cpython-39.pyc delete mode 100644 python/__pycache__/plot.cpython-312.pyc delete mode 100644 python/__pycache__/plot.cpython-39.pyc delete mode 100644 python/__pycache__/slidingWindow.cpython-312.pyc delete mode 100644 python/__pycache__/slidingWindow.cpython-39.pyc delete mode 100644 python/__pycache__/svgFactory.cpython-312.pyc diff --git a/.gitignore b/.gitignore index abd974d..9810f5a 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ js/* !python python/sample_composites/composite_average.out /python/sample_composites +/python/__pycache__ \ No newline at end of file diff --git a/js/events/load_composite_button.js b/js/events/load_composite_button.js index c9dd1a4..85b0e25 100644 --- a/js/events/load_composite_button.js +++ b/js/events/load_composite_button.js @@ -19,7 +19,6 @@ $(function() { $("#metadata-table").metadata_table("add_row", [id]); $("#settings-table").settings_table("add_row", [id]); }; - console.log(prefixes) $("#settings-table").settings_table("plot_all_composites", {xmin: xmin, xmax: xmax, ymax: ymax}, allow_shrink=true); $("#main-plot").main_plot("update_legend") diff --git a/js/parse_composite.js b/js/parse_composite.js index fbba6fd..3dde9e8 100644 --- a/js/parse_composite.js +++ b/js/parse_composite.js @@ -129,7 +129,6 @@ let parse_multiple_composite = function(text, prefix) { if (col0 === "" || col0 === "NAME") { // If the x domain is defined, save the composite if (save_comp) { - console.log(id) composites[id] = {xmin: xmin, xmax: xmax, sense: sense, anti: anti} }; save_comp = false; @@ -143,7 +142,6 @@ let parse_multiple_composite = function(text, prefix) { } } else if (col0.startsWith(prefix)){ id = col0.slice(prefix.length).split("_")[0]; - console.log(id) save_comp = true; if (col0.toLowerCase().includes("sense")) { sense = fields.slice(1).map(parseFloat) @@ -162,6 +160,5 @@ let parse_multiple_composite = function(text, prefix) { if (save_comp) { composites[id] = {xmin: xmin, xmax: xmax, sense: sense, anti: anti} }; - console.log(composites) return composites } \ No newline at end of file diff --git a/js/widgets/main_plot.js b/js/widgets/main_plot.js index e15c5e4..d6f9ce1 100644 --- a/js/widgets/main_plot.js +++ b/js/widgets/main_plot.js @@ -315,8 +315,6 @@ $(function() { plot_composite: function(xmin, xmax, sense, anti, scale, color, secondary_color, i, opacity, smoothing, bp_shift, hide, hide_sense=false, hide_anti=false, baseline=0) { // Set composite visibility - console.log("xmin:" + xmin) - console.log("xmax:" + xmax) let composite = this._elements.composites[i] .classed("plotted", !hide) .style("display", hide ? 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z5q6j#v4L0upN$d+$r;#=?i3`^sr2`HtycT3#`3Mk@tvmOJ59^C8qen>&-)iha nedV_r^LLucCzk5#UC8l&aBva(A26-e+JCsDe^;xm5}5oy32Y6O diff --git a/python/plot.py b/python/plot.py index fd9832e..7360905 100644 --- a/python/plot.py +++ b/python/plot.py @@ -405,9 +405,20 @@ def import_data(self, file, args, import_composites): # Add _imported to composite name if duplicate of existing composite if any(n == self.composites[j].name for j in range(len(self.composites))): n = str(n) + "_imported" - self.composites.append(composite.Composite(scale=c.get('scale'), color=c.get('color'), secondary_color=c.get('secondary-color'), opacity=c.get('opacity'), - smoothing=c.get('smoothing'), bp_shift=c.get('bp_shift'), hide_sense=c.get('hide_sense'), hide_anti=c.get('hide_anti'), - baseline=c.get('baseline'), name=n, sense=c.get('sense'), anti=c.get('anti'), xmin=c.get('xmin'), xmax=c.get('xmax'))) + self.composites.append(composite.Composite(scale=float(c.get('scale')) if c.get('scale') is not None else None, + color=c.get('color'), + secondary_color=c.get('secondary_color'), + opacity=c.get('opacity') if c.get('smoothing') != False else None, + smoothing=c.get('smoothing') if c.get('smoothing') != False else None, + bp_shift=c.get('bp_shift') if c.get('bp_shift') != False else None, + hide_sense=hide if (hide := c.get('hide')) == True else c.get('hide_forward'), + hide_anti=hide if hide == True else c.get('hide_reverse'), + baseline=c.get('baseline'), + name=n, + sense=c.get('sense'), + anti=c.get('anti'), + xmin=c.get('xmin'), + xmax=c.get('xmax'))) plot_data = data['plot'] # Add plot variables self.title = plot_data.get('title', self.title) if args.title is None else self.title diff --git a/python/plotter.py b/python/plotter.py index 45a63e6..0bf5d6b 100644 --- a/python/plotter.py +++ b/python/plotter.py @@ -96,7 +96,7 @@ def main(): smoothing=args.smoothing, bp_shift=args.bp_shift, hide_sense= args.hide_sense, hide_anti= args.hide_anti, baseline=args.shift_occupancy, name=args.name if args.name is not None else names[i], opacity=args.opacity,) - composite_files = args.files.split("-") + composite_files = args.files.split(":") for c in composite_files: #Check if composite file contains multiple composites if sum(1 for line in open(c) if len(line.strip()) != 0) <= 3: diff --git a/python/readme.md b/python/readme.md index a749f58..5da10d4 100644 --- a/python/readme.md +++ b/python/readme.md @@ -54,7 +54,7 @@ The available options for the `plot` subcommand are: composite [file] [composite options] ``` -The `composite` subcommand takes a positional argument that specifies the files to be loaded into the composite. If there are multiple files, they should be separated by a "-". For example, `composite sample1.out-sample2.out-sample3.out --opacity 0.5` loads samples 1-3 into the composite and sets the maximum opacity to 0.5. +The `composite` subcommand takes a positional argument that specifies the files to be loaded into the composite. If there are multiple files, they should be separated by a ":". For example, `composite sample1.out-sample2.out-sample3.out --opacity 0.5` loads samples 1-3 into the composite and sets the maximum opacity to 0.5. The available options for the `composite` subcommand are: diff --git a/python/slidingWindow.py b/python/slidingWindow.py index 0a5781b..99c287b 100644 --- a/python/slidingWindow.py +++ b/python/slidingWindow.py @@ -1,7 +1,6 @@ # Copy of sliding_window from plotter def sliding_window(xdomain, occupancy, window): occupancy_val = sum(occupancy[:window]) / window - print("length: " + str(xdomain)) new_xdomain = [(xdomain[0] + xdomain[window - 1]) / 2] new_occupancy = [occupancy_val]