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"""
Logo formatting. Each formatter is a function f(data, format) that draws
a representation of the logo. The main graphical formatter is eps_formatter. A mapping
'formatters' containing all available formatters . Each formatter returns binary data. The eps
and data formats can decoded to strings, e.g. eps_as_string = eps_data.decode()
"""
import os
import shutil
from math import log
from string import Template
from subprocess import PIPE, Popen
from typing import Optional
from .color import Color
from .logo import LogoData, LogoFormat
from .utils import resource_string
__all__ = [
"pdf_formatter",
"jpeg_formatter",
"svg_formatter",
"png_print_formatter",
"txt_formatter",
"eps_formatter",
"formatters",
"default_formatter",
"GhostscriptAPI",
]
std_units = {
"bits": 1.0 / log(2),
"nats": 1.0,
"digits": 1.0 / log(10),
"kT": 1.0,
"kJ/mol": 8.314472 * 298.15 / 1000.0,
"kcal/mol": 1.987 * 298.15 / 1000.0,
"probability": None,
}
"""Some text"""
def pdf_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Generate a logo in PDF format."""
eps = eps_formatter(logodata, logoformat).decode()
gs = GhostscriptAPI()
assert logoformat.logo_height is not None
assert logoformat.logo_width is not None
return gs.convert("pdf", eps, logoformat.logo_width, logoformat.logo_height)
def _bitmap_formatter(logodata: LogoData, logoformat: LogoFormat, device: str) -> bytes:
eps = eps_formatter(logodata, logoformat).decode()
gs = GhostscriptAPI()
return gs.convert(
device,
eps,
logoformat.logo_width,
logoformat.logo_height,
logoformat.resolution,
)
def jpeg_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Generate a logo in JPEG format."""
return _bitmap_formatter(logodata, logoformat, device="jpeg")
def svg_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Generate a logo in Scalable Vector Graphics (SVG) format.
Requires the program 'pdf2svg' be installed.
"""
pdf = pdf_formatter(logodata, logoformat)
command = shutil.which("pdf2svg")
if command is None:
raise EnvironmentError(
"Scalable Vector Graphics (SVG) format requires the program" "'pdf2svg'."
) # pragma: no cover
import tempfile
fpdfi, fname_pdf = tempfile.mkstemp(suffix=".pdf")
fsvgi, fname_svg = tempfile.mkstemp(suffix=".svg")
try:
fpdf2 = open(fname_pdf, "w")
fpdf2.buffer.write(pdf)
fpdf2.seek(0)
args = [command, fname_pdf, fname_svg]
p = Popen(args)
(out, err) = p.communicate()
fsvg = open(fname_svg)
return fsvg.read().encode()
finally:
os.remove(fname_svg)
os.remove(fname_pdf)
# def png_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
# """Generate a logo in PNG format."""
# return _bitmap_formatter(logodata, logoformat, device="png")
def png_print_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Generate a logo in PNG format with print quality (600 DPI) resolution."""
logoformat.resolution = 600
return _bitmap_formatter(logodata, logoformat, device="png")
def txt_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Create a text representation of the logo data."""
return str(logodata).encode()
def csv_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Create a csv representation of the logo data."""
return logodata.csv().encode()
def eps_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes:
"""Generate a logo in Encapsulated Postscript (EPS)"""
substitutions = {}
from_format = [
"creation_date",
"logo_width",
"logo_height",
"lines_per_logo",
"line_width",
"line_height",
"line_margin_right",
"line_margin_left",
"line_margin_bottom",
"line_margin_top",
"title_height",
"xaxis_label_height",
"creator_text",
"logo_title",
"logo_margin",
"stroke_width",
"tic_length",
"stacks_per_line",
"stack_margin",
"yaxis_label",
"yaxis_tic_interval",
"yaxis_minor_tic_interval",
"xaxis_label",
"xaxis_tic_interval",
"number_interval",
"fineprint",
"shrink_fraction",
"errorbar_fraction",
"errorbar_width_fraction",
"errorbar_gray",
"small_fontsize",
"fontsize",
"title_fontsize",
"number_fontsize",
"text_font",
"logo_font",
"title_font",
"logo_label",
"yaxis_scale",
"end_type",
"debug",
"show_title",
"show_xaxis",
"show_xaxis_label",
"show_yaxis",
"show_yaxis_label",
"show_boxes",
"show_errorbars",
"show_fineprint",
"rotate_numbers",
"show_ends",
"stack_height",
"stack_width",
]
for sf in from_format:
substitutions[sf] = getattr(logoformat, sf)
substitutions["shrink"] = str(logoformat.show_boxes).lower()
def format_color(color: Color) -> str: # (no fold)
return " ".join(("[", str(color.red), str(color.green), str(color.blue), "]"))
substitutions["default_color"] = format_color(logoformat.default_color)
data = []
# Unit conversion. 'None' for probability units
conv_factor = std_units[logoformat.unit_name]
data.append("StartLine")
# assert checks for logoformat attributes that are intialized to None
assert logoformat.logo_start is not None
assert logoformat.first_index is not None
assert logoformat.logo_end is not None
seq_from = logoformat.logo_start - logoformat.first_index
seq_to = logoformat.logo_end - logoformat.first_index + 1
# seq_index : zero based index into sequence data
# logo_index : User visible coordinate, first_index based
# stack_index : zero based index of visible stacks
for seq_index in range(seq_from, seq_to):
# logo_index = seq_index + logoformat.first_index
stack_index = seq_index - seq_from
if stack_index != 0 and (stack_index % logoformat.stacks_per_line) == 0:
data.append("")
data.append("EndLine")
data.append("StartLine")
data.append("")
data.append("(%s) StartStack" % logoformat.annotate[seq_index])
if conv_factor:
assert logodata.entropy is not None
assert logoformat.unit_name is not None
stack_height = logodata.entropy[seq_index] * std_units[logoformat.unit_name]
else:
stack_height = 1.0 # probability # pragma: no cover
# Sort by frequency. If equal frequency then reverse alphabetic
# (So sort reverse alphabetic first, then frequency)
# TODO: doublecheck this actual works
assert logodata.alphabet is not None
assert logodata.counts is not None
s = list(zip(logodata.counts[seq_index], logodata.alphabet))
s.sort(key=lambda x: x[1])
s.reverse()
s.sort(key=lambda x: x[0])
if not logoformat.reverse_stacks:
s.reverse() # pragma: no cover
C = float(sum(logodata.counts[seq_index]))
if C > 0.0:
fraction_width = 1.0
assert logoformat.scale_width is not None
if logoformat.scale_width:
assert logodata.weight is not None
fraction_width = float(logodata.weight[seq_index])
for rank, c in enumerate(s):
assert logoformat.color_scheme is not None
color = logoformat.color_scheme.symbol_color(seq_index, c[1], rank)
data.append(
" %f %f %s (%s) ShowSymbol"
% (
fraction_width,
c[0] * stack_height / C,
format_color(color),
c[1],
)
)
# Draw error bar on top of logo. Replaced by DrawErrorbarFirst above.
if logodata.entropy_interval is not None and conv_factor and C > 0.0:
low, high = logodata.entropy_interval[seq_index]
assert logodata.entropy is not None
center = logodata.entropy[seq_index]
low *= conv_factor
high *= conv_factor
center *= conv_factor
if high > logoformat.yaxis_scale:
high = logoformat.yaxis_scale # pragma: no cover
down = center - low
up = high - center
data.append(" %f %f DrawErrorbar" % (down, up))
data.append("EndStack")
data.append("")
data.append("EndLine")
substitutions["logo_data"] = "\n".join(data)
# Create and output logo
template = resource_string(__name__, "template.eps", __file__).decode()
logo = Template(template).substitute(substitutions)
return logo.encode()
formatters = {
"eps": eps_formatter,
"pdf": pdf_formatter,
"png": png_print_formatter,
"png_print": png_print_formatter,
"jpeg": jpeg_formatter,
"svg": svg_formatter,
"logodata": txt_formatter,
"csv": csv_formatter,
}
"""Map between output format names and corresponding logo formatter"""
default_formatter = eps_formatter
"""The default logo formatter."""
class GhostscriptAPI:
"""Interface to the command line program Ghostscript ('gs')"""
formats = ("png", "pdf", "jpeg")
def __init__(self, path: Optional[os.PathLike] = None) -> None:
"""
Raises:
EnvironmentError: If cannot find Ghostscript executable on
path
"""
command = shutil.which("gs", path=path)
if command is None:
command = shutil.which("gswin64c.exe", path=path) # pragma: no cover
if command is None:
command = shutil.which("gswin32c.exe", path=path) # pragma: no cover
if command is None:
raise EnvironmentError(
"Could not find Ghostscript on path. "
"There should be either a gs executable or a gswin32c.exe on "
"your system's path"
) # pragma: no cover
self.command = command
def version(self) -> bytes:
"""Returns: The ghostscript version string"""
args = [self.command, "--version"]
try:
p = Popen(args, stdout=PIPE)
(out, err) = p.communicate()
except OSError: # pragma: no cover
raise RuntimeError(
"Cannot communicate with ghostscript."
) # pragma: no cover
return out.strip()
def convert(
self,
format: str,
postscript: str,
width: Optional[int],
height: Optional[int],
resolution: int = 300,
) -> bytes:
"""Convert a string of postscript into a different graphical format
Supported formats are 'png', 'pdf', and 'jpeg'.
Raises:
ValueError: For an unrecognized format.
"""
device_map = {"png": "png16m", "pdf": "pdfwrite", "jpeg": "jpeg"}
try:
device = device_map[format]
except KeyError: # pragma: no cover
raise ValueError("Unsupported format.")
args = [
self.command,
"-sDEVICE=%s" % device,
"-dPDFSETTINGS=/printer",
# "-q", # Quite: Do not dump messages to stdout.
"-sstdout=%stderr", # Redirect messages and errors to stderr
# fix issue 36, problems with ghostscript 9.10
"-dColorConversionStrategy=/LeaveColorUnchanged",
"-sOutputFile=-", # Stdout
"-dDEVICEWIDTHPOINTS=%s" % str(width),
"-dDEVICEHEIGHTPOINTS=%s" % str(height),
"-dSAFER", # For added security
"-dNOPAUSE",
]
if device != "pdf":
args.append("-r%s" % str(resolution))
assert resolution is not None
if resolution < 300: # Antialias if resolution is Less than 300 DPI
args.append("-dGraphicsAlphaBits=4")
args.append("-dTextAlphaBits=4")
args.append("-dAlignToPixels=0")
args.append("-") # Read from stdin. Must be last argument.
error_msg = (
"Unrecoverable error : Ghostscript conversion failed "
"(Invalid postscript?). %s" % " ".join(args)
)
try:
p = Popen(args, stdin=PIPE, stdout=PIPE, stderr=PIPE)
(out, err) = p.communicate(postscript.encode())
except OSError: # pragma: no cover
raise RuntimeError(error_msg) # pragma: no cover
if p.returncode != 0: # pragma: no cover
error_msg += "\nReturn code: %i\n" % p.returncode
if err is not None:
error_msg += str(err)
raise RuntimeError(error_msg)
return out
# end class Ghostscript
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