Code cleanup and documentation
This commit is contained in:
Landon Wark
@@ -2,5 +2,3 @@
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Contains all operations for creating charts, graphs and visual effects.
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'''
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from .control_charts import *
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from .barcode import *
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from .plate_map import *
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@@ -1,19 +0,0 @@
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from reportlab.graphics.barcode import createBarcodeImageInMemory
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from reportlab.graphics.shapes import Drawing
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from reportlab.lib.units import mm
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def make_plate_barcode(text:str, width:int=100, height:int=25) -> Drawing:
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"""
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Creates a barcode image for a given str.
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Args:
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text (str): Input string
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width (int, optional): Width (pixels) of image. Defaults to 100.
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height (int, optional): Height (pixels) of image. Defaults to 25.
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Returns:
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Drawing: image object
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"""
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# return createBarcodeDrawing('Code128', value=text, width=200, height=50, humanReadable=True)
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return createBarcodeImageInMemory('Code128', value=text, width=width*mm, height=height*mm, humanReadable=True, format="png")
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@@ -12,7 +12,6 @@ from frontend.widgets.functions import select_save_file
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logger = logging.getLogger(f"submissions.{__name__}")
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def create_charts(ctx:Settings, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
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"""
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Constructs figures based on parsed pandas dataframe.
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@@ -40,7 +39,6 @@ def create_charts(ctx:Settings, df:pd.DataFrame, ytitle:str|None=None) -> Figure
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genera.append("")
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df['genus'] = df['genus'].replace({'\*':''}, regex=True).replace({"NaN":"Unknown"})
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df['genera'] = genera
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# df = df.dropna()
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# remove original runs, using reruns if applicable
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df = drop_reruns_from_df(ctx=ctx, df=df)
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# sort by and exclude from
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@@ -224,4 +222,4 @@ def construct_html(figure:Figure) -> str:
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else:
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html += "<h1>No data was retrieved for the given parameters.</h1>"
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html += '</body></html>'
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return html
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return html
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@@ -1,121 +0,0 @@
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from pathlib import Path
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from PIL import Image, ImageDraw, ImageFont
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import numpy as np
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from tools import check_if_app, jinja_template_loading
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import logging, sys
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logger = logging.getLogger(f"submissions.{__name__}")
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def make_plate_map(sample_list:list) -> Image:
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"""
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Makes a pillow image of a plate from hitpicks
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Args:
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sample_list (list): list of sample dictionaries from the hitpicks
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Returns:
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Image: Image of the 96 well plate with positive samples in red.
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"""
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# If we can't get a plate number, do nothing
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try:
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plate_num = sample_list[0]['plate_name']
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except IndexError as e:
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logger.error(f"Couldn't get a plate number. Will not make plate.")
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return None
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except TypeError as e:
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logger.error(f"No samples for this plate. Nothing to do.")
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return None
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# Make an 8 row, 12 column, 3 color ints array, filled with white by default
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grid = np.full((8,12,3),255, dtype=np.uint8)
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# Go through samples and change its row/column to red if positive, else blue
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for sample in sample_list:
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logger.debug(f"sample keys: {list(sample.keys())}")
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# set color of square
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if sample['positive']:
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colour = [255,0,0]
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else:
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if 'colour' in sample.keys():
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colour = sample['colour']
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else:
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colour = [0,0,255]
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grid[int(sample['row'])-1][int(sample['column'])-1] = colour
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# Create pixel image from the grid and enlarge
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img = Image.fromarray(grid).resize((1200, 800), resample=Image.NEAREST)
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# create a drawer over the image
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draw = ImageDraw.Draw(img)
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# draw grid over the image
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y_start = 0
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y_end = img.height
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step_size = int(img.width / 12)
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for x in range(0, img.width, step_size):
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line = ((x, y_start), (x, y_end))
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draw.line(line, fill=128)
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x_start = 0
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x_end = img.width
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step_size = int(img.height / 8)
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for y in range(0, img.height, step_size):
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line = ((x_start, y), (x_end, y))
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draw.line(line, fill=128)
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del draw
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old_size = img.size
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new_size = (1300, 900)
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# create a new, larger white image to hold the annotations
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new_img = Image.new("RGB", new_size, "White")
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box = tuple((n - o) // 2 for n, o in zip(new_size, old_size))
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# paste plate map into the new image
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new_img.paste(img, box)
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# create drawer over the new image
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draw = ImageDraw.Draw(new_img)
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if check_if_app():
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font_path = Path(sys._MEIPASS).joinpath("files", "resources")
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else:
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font_path = Path(__file__).parents[2].joinpath('resources').absolute()
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logger.debug(f"Font path: {font_path}")
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font = ImageFont.truetype(font_path.joinpath('arial.ttf').__str__(), 32)
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row_dict = ["A", "B", "C", "D", "E", "F", "G", "H"]
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# write the plate number on the image
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draw.text((100, 850),plate_num,(0,0,0),font=font)
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# write column numbers
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for num in range(1,13):
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x = (num * 100) - 10
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draw.text((x, 0), str(num), (0,0,0),font=font)
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# write row letters
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for num in range(1,9):
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letter = row_dict[num-1]
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y = (num * 100) - 10
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draw.text((10, y), letter, (0,0,0),font=font)
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return new_img
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def make_plate_map_html(sample_list:list, plate_rows:int=8, plate_columns=12) -> str:
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"""
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Constructs an html based plate map.
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Args:
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sample_list (list): List of submission samples
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plate_rows (int, optional): Number of rows in the plate. Defaults to 8.
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plate_columns (int, optional): Number of columns in the plate. Defaults to 12.
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Returns:
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str: html output string.
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"""
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for sample in sample_list:
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if sample['positive']:
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sample['background_color'] = "#f10f07"
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else:
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if "colour" in sample.keys():
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sample['background_color'] = "#69d84f"
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else:
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sample['background_color'] = "#80cbc4"
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output_samples = []
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for column in range(1, plate_columns+1):
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for row in range(1, plate_rows+1):
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try:
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well = [item for item in sample_list if item['row'] == row and item['column']==column][0]
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except IndexError:
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well = dict(name="", row=row, column=column, background_color="#ffffff")
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output_samples.append(well)
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env = jinja_template_loading()
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template = env.get_template("plate_map.html")
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html = template.render(samples=output_samples, PLATE_ROWS=plate_rows, PLATE_COLUMNS=plate_columns)
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return html
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