showing print parameters on report

.gitignore

@@ -1,6 +1,9 @@
 # example data
 example 1/
 example 2/
+example fail 1/
+example fail 2/
+example fail 3/
 
 # ---> Python
 # Byte-compiled / optimized / DLL files

s3printlog/__init__.py

@@ -1 +1,2 @@
 from . import gui
+from . import main

s3printlog/gui.py

@@ -5,8 +5,7 @@ import tkinter.ttk as ttk
 from pathlib import Path
 from tkinter import filedialog
 
-from .logparser import get_log_files, DROP_CHECK_SUFFIX, ENVIRONMENT_SUFFIX
-from .main import process_log_folder, open_with_default_app
+from .main import get_log_files, process_log_folder, open_with_default_app
 
 
 if getattr(sys, "frozen", False):
@@ -20,16 +19,6 @@ else:
     icon_path = None
 
 
-def validate_folder(folder):
-    dir_path = Path(folder)
-    drop_checks = get_log_files(dir_path, DROP_CHECK_SUFFIX)
-    env_log = get_log_files(dir_path, ENVIRONMENT_SUFFIX)
-    if drop_checks and env_log:
-        return folder
-    else:
-        return None
-
-
 class StatusPanel(tk.Frame):
     def __init__(self, parent):
         tk.Frame.__init__(self, parent.master)
@@ -89,7 +78,7 @@ class Application(tk.Frame):
         master.minsize(height=150, width=400)
         tk.Frame.__init__(self, master)
         self._master = master
-        self.selected_folder = None
+        self.log_files = None
         self.pack(fill=tk.BOTH)
         self.file_panel = FilePanel(self)
         self.action_panel = ActionPanel(self)
@@ -105,12 +94,12 @@ class Application(tk.Frame):
         opts = {"initialdir": "~/Desktop", "mustexist": True}
         selection = tk.filedialog.askdirectory(**opts)
         if selection:
-            self.selected_folder = validate_folder(selection)
+            self.log_files = get_log_files(selection)
         self.set_active_state()
 
     def set_active_state(self, event=None):
-        if self.selected_folder is not None:
-            self.file_panel.set_text(self.selected_folder)
+        if self.log_files:
+            self.file_panel.set_text(self.log_files.folder)
             self.action_panel.enable()
         else:
             self.file_panel.set_text("This is not a S3 Print Log Folder")
@@ -123,7 +112,7 @@ class Application(tk.Frame):
         self.status_panel.set_text(
             "Generating report, PDF should be opened in a couple of seconds"
         )
-        report_file = process_log_folder(self.selected_folder)
+        report_file = process_log_folder(self.log_files)
         open_with_default_app(report_file)
         self.status_panel.set_text("Report Generated.")
 

s3printlog/logparser.py

@@ -10,8 +10,8 @@ from collections import namedtuple
 from enum import Enum
 from io import StringIO
 
-DROP_CHECK_SUFFIX = ".cor"
-ENVIRONMENT_SUFFIX = "_Logfile.log"
+
+PrintLogResult = namedtuple("PrintLogResult", ["environment", "info"])
 
 
 class CheckWhen(Enum):
@@ -25,7 +25,7 @@ class CheckResult(Enum):
     SKIPPED = "skipped"
 
 
-class LogResult:
+class DropCheckResult:
     def __init__(
         self,
         path,
@@ -101,18 +101,13 @@ def parse_log_line(line, cast_to, default_value=np.nan, separator="="):
     return parse_str_value(str_data, cast_to, default_value)
 
 
-def get_log_files(folder, suffix=".cor"):
-    visible = (p for p in folder.iterdir() if not p.name.startswith("."))
-    return [p for p in visible if p.name.endswith(suffix)]
-
-
 def parse_log_files(log_list):
     pre_run = dict()
     post_run = dict()
     well_list = list()
     # use the files sorted by date and time
     for path in sorted(log_list):
-        log_result = LogResult.from_file(path)
+        log_result = DropCheckResult.from_file(path)
         if log_result.well not in pre_run:
             log_result.when = CheckWhen.PRE_RUN
             pre_run[log_result.well] = log_result
@@ -125,7 +120,9 @@ def parse_log_files(log_list):
 
     skipped_runs = {well for well in pre_run if well not in post_run}
     for well in skipped_runs:
-        post_result = LogResult("", well, CheckResult.SKIPPED, when=CheckWhen.POST_RUN)
+        post_result = DropCheckResult(
+            "", well, CheckResult.SKIPPED, when=CheckWhen.POST_RUN
+        )
         post_run[well] = post_result
 
     parsed_files = []
@@ -136,12 +133,53 @@ def parse_log_files(log_list):
     return pd.DataFrame([pf.as_dict() for pf in parsed_files])
 
 
-def parse_environment_log(log_file_path):
-    with open(log_file_path, "r", encoding="iso-8859-1") as file_handle:
-        env_lines = [l for l in file_handle if "\tHumidity=\t" in l]
+def split_print_log_line(line):
+    _, value = line.split(":", 1)
+    return value.strip()
+
+
+def count_solutions(file_handle):
+    solutions = set()
+    for line in file_handle:
+        line = line.strip()
+        if not line or line[0] in ("X", "Y", "F", "["):
+            # empty line or uninteresting one, pick next one
+            continue
+        elif line.startswith("Drops/Field"):
+            # finished with all field definition, leave loop
+            break
+        entries = (item.strip() for item in line.split("\t"))
+        wells = (well for well in entries if well)
+        solutions.update(wells)
+    return len(solutions)
+
+
+def parse_print_log(log_files):
+    env_lines = []
+    print_info = {}
+    with open(log_files, "r", encoding="iso-8859-1") as file_handle:
+        for line in file_handle:
+            if "\tHumidity=\t" in line:
+                env_lines.append(line)
+            elif line.startswith("Probe:"):
+                print_info["source"] = split_print_log_line(line)
+            elif line.startswith("Target:"):
+                target_and_fields = split_print_log_line(line)
+                target, fields = target_and_fields.rsplit(":", 1)
+                print_info["target"] = target.strip()
+                print_info["fields"] = len(fields.split(","))
+            elif line.startswith("Humidity:"):
+                print_info["humidity"] = split_print_log_line(line)
+            elif line.startswith("Run Name:"):
+                print_info["run"] = split_print_log_line(line)
+            elif line.startswith("Dot Pitch:"):
+                # important to pass the filehandle iterator here
+                print_info["solutions"] = count_solutions(file_handle)
+
     buff = StringIO("".join(env_lines))
     columns = ["datetime", "garbage 1", "humidity", "garbage 2", "temperature"]
-    df = pd.read_csv(
+    tmp_df = pd.read_csv(
         buff, sep="\t", header=None, names=columns, index_col=0, parse_dates=True
     )
-    return df.drop(columns=["garbage 1", "garbage 2"])
+    environment_df = tmp_df.drop(columns=["garbage 1", "garbage 2"])
+    return PrintLogResult(environment_df, print_info)

s3printlog/main.py

@@ -12,36 +12,48 @@ from .analysis import (
     generate_environment_graph,
     find_missing_drops,
 )
-from .logparser import (
-    get_log_files,
-    parse_log_files,
-    parse_environment_log,
-    DROP_CHECK_SUFFIX,
-    ENVIRONMENT_SUFFIX,
-)
+from .logparser import parse_log_files, parse_print_log
 from .report import generate_report
 
+DROP_CHECK_SUFFIX = ".cor"
+ENVIRONMENT_SUFFIX = "_Logfile.log"
+
+
+DropProcessResult = namedtuple("DropProcessResult", ["drops", "missing"])
+PrintLogResult = namedtuple("PrintLogResult", ["environment", "info"])
+ProcessResult = namedtuple("ProcessResult", ["data_frame", "file_path"])
+
+
+class LogFiles(namedtuple("LogFiles", ["folder", "drop_check", "environment"])):
+    __slots__ = ()
+
+    def __bool__(self):
+        return self.drop_check and self.environment
+
 
 class NoLogFileError(IOError):
     pass
 
 
-ProcessResult = namedtuple("ProcessResult", ["data_frame", "file_path"])
-DropProcessResult = namedtuple("DropProcessResult", ["drops", "missing"])
+def get_log_files(folder):
+    folder = pathlib.Path(folder)
+    visible = [p for p in folder.iterdir() if not p.name.startswith(".")]
+    drop_files = [p for p in visible if p.name.endswith(DROP_CHECK_SUFFIX)]
+    env_files = [p for p in visible if p.name.endswith(ENVIRONMENT_SUFFIX)]
+    if len(env_files) != 1:
+        env_files = [None]
+    return LogFiles(folder, drop_files, env_files[0])
 
 
-def process_drop_checks(folder):
-    drop_log_paths = get_log_files(folder, suffix=DROP_CHECK_SUFFIX)
-    if len(drop_log_paths) == 0:
-        raise NoLogFileError("Drop Check Files Not Found")
-    drop_log_df = parse_log_files(drop_log_paths)
+def process_drop_checks(log_files):
+    drop_log_df = parse_log_files(log_files.drop_check)
 
     generate_drop_check_chart(drop_log_df)
-    image_path = folder / "Drop Check.png"
+    image_path = log_files.folder / f"{log_files.folder}_drop_check.png"
     plt.savefig(image_path)
 
     missing_drop_df = find_missing_drops(drop_log_df)
-    misssing_drop_list_path = folder / "Missed spots.xlsx"
+    misssing_drop_list_path = log_files.folder / f"{log_files.folder}_missed_spots.xlsx"
     missing_drop_df.to_excel(misssing_drop_list_path)
 
     return DropProcessResult(
@@ -50,26 +62,29 @@ def process_drop_checks(folder):
     )
 
 
-def process_environment(folder):
-    env_log_paths = get_log_files(folder, suffix=ENVIRONMENT_SUFFIX)
-    if len(env_log_paths) != 1:
-        raise NoLogFileError("Log File Not Found")
-    env_log_df = parse_environment_log(env_log_paths[0])
+def process_print_log(log_files):
+    print_log = parse_print_log(log_files.environment)
 
-    generate_environment_graph(env_log_df)
-    image_path = folder / "Environment.png"
+    generate_environment_graph(print_log.environment)
+    image_path = log_files.folder / f"{log_files.folder}_environment.png"
     plt.savefig(image_path)
 
-    return ProcessResult(env_log_df, image_path)
+    return PrintLogResult(ProcessResult(print_log.environment, image_path), print_log.info)
 
 
 def process_log_folder(folder):
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
-        folder = pathlib.Path(folder)
-        drops, missing = process_drop_checks(folder)
-        environment = process_environment(folder)
-        return generate_report(folder, drops, missing, environment)
+        log_files = get_log_files(folder)
+        drop_check_result = process_drop_checks(log_files)
+        print_log_result = process_print_log(log_files)
+        return generate_report(
+            log_files,
+            drop_check_result.drops,
+            drop_check_result.missing,
+            print_log_result.environment,
+            print_log_result.info,
+        )
 
 
 def open_with_default_app(some_path):

s3printlog/report.py

@@ -15,12 +15,14 @@ from reportlab.platypus import (
     Paragraph,
     Spacer,
     SimpleDocTemplate,
+    Table,
 )
 
 
 ImageBuffer = namedtuple("ImageBuffer", ["buffer", "width", "height"])
 FailedDropImage = namedtuple("FailedDropImage", ["path", "well"])
 
+
 styles = getSampleStyleSheet()
 style_n = styles["Normal"]
 style_h1 = styles["Heading1"]
@@ -110,7 +112,31 @@ def failed_drops_flowable(drops, missing, what):
     return section
 
 
-def generate_report(folder, drops, missing, environment):
+def print_info_flowable(print_info):
+    data = [
+        ("Source Plate:", print_info["source"]),
+        ("Print Solutions:", f"{print_info['solutions']} different solutions"),
+        ("Target Substrate:", print_info["target"]),
+        ("Number of Fields:", f"{print_info['fields']} fields printed"),
+        ("Run Method:", print_info["run"]),
+        (
+            "Humidity Setting:",
+            f"{print_info['humidity']} (humidifier might be turned off)",
+        ),
+    ]
+    # Table(data, colWidths=None, rowHeights=None, style=None, splitByRow=1,
+    # repeatRows=0, repeatCols=0, rowSplitRange=None, spaceBefore=None,
+    # spaceAfter=None)
+    return Table(data, style=[
+        ('TOPPADDING', (0, 0), (-1, -1), 1),
+        ('RIGHTPADDING', (0, 0), (-1, -1), 7),
+        ('BOTTOMPADDING', (0, 0), (-1, -1), 1),
+        ('LEFTPADDING', (0, 0), (-1, -1), 0),
+],hAlign='LEFT'
+        )
+
+
+def generate_report(log_files, drops, missing, environment, print_info):
 
     story = []
 
@@ -122,12 +148,15 @@ def generate_report(folder, drops, missing, environment):
     story.append(headline)
     story.append(Spacer(width=17 * cm, height=0.5 * cm))
 
+    story.append(print_info_flowable(print_info))
+    story.append(Spacer(width=17 * cm, height=0.5 * cm))
+
     story.append(graph_flowable("Drop Check Graphs", drops.file_path))
 
     story.extend(failed_drops_flowable(drops, missing, "pre run"))
     story.extend(failed_drops_flowable(drops, missing, "post run"))
 
-    if len(story) == 3:
+    if len(story) == 5:
         # no failed drop checks where reported
         story.append(Spacer(width=17 * cm, height=1 * cm))
         story.append(Paragraph("No failed drop checks found.", style_n))
@@ -135,7 +164,7 @@ def generate_report(folder, drops, missing, environment):
     story.append(PageBreak())
     story.append(graph_flowable("Environment Graphs", environment.file_path))
 
-    pdf_path = folder / "print_report.pdf"
+    pdf_path = log_files.folder / f"{log_files.folder}_report.pdf"
     doc = SimpleDocTemplate(
         str(pdf_path),
         pagesize=A4,

test.py

@@ -0,0 +1,12 @@
+# import s3printlog
+# s3printlog.run("example 1")
+
+from s3printlog import main
+
+folder = "example 1"
+#folder = "example 2"
+
+print("Generating report, PDF should be opened in a couple of seconds")
+report_file = main.process_log_folder(folder)
+main.open_with_default_app(report_file)
+print("Report Generated.")