petal-qc 0.0.0__py3-none-any.whl

petal_qc/metrology/coreMetrology.py

@@ -0,0 +1,402 @@
+#!/usr/bin/env python3
+"""GUI to launch metrology analysis."""
+from pathlib import Path
+from argparse import Action
+from argparse import ArgumentParser
+import itkdb_gtk.ITkDButils
+import itkdb_gtk.dbGtkUtils
+import numpy as np
+from contextlib import redirect_stdout
+import itkdb_gtk
+import itkdb_gtk.UploadTest
+
+from petal_qc.metrology.do_Metrology import do_analysis
+
+import gi
+gi.require_version("Gtk", "3.0")
+from gi.repository import Gtk, GObject, Gio, GLib
+
+
+
+class CommaSeparatedListAction(Action):
+    """Create a list from the comma sepparated numbers at imput."""
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        """The actual action."""
+        value = np.array(list(map(float, values.split(','))), dtype='float64')
+        if value.shape[0] < 3:
+            raise Exception("{} needs a 3D vector".format(self.dest))
+
+        setattr(namespace, self.dest, value)
+
+
+class CoreMetrology(itkdb_gtk.dbGtkUtils.ITkDBWindow):
+    """Application window."""
+
+    def __init__(self, options, session=None, title="",  panel_size=100):
+        """Initialization.
+
+        Args:
+            title: The title of the window.
+            pannel_size: size of message panel.
+
+        """
+        super().__init__(session=session, title=title)
+
+        self.data_file = None
+        self.folder = None
+        self.petal_SN = None
+        self.petal_prefix = None
+        self.options = options
+        self.alternativeID = None
+        self.outDB = None
+
+
+        # Active button in header
+        button = Gtk.Button()
+        icon = Gio.ThemedIcon(name="document-send-symbolic")
+        image = Gtk.Image.new_from_gicon(icon, Gtk.IconSize.BUTTON)
+        button.add(image)
+        button.set_tooltip_text("Click to upload test")
+        button.connect("clicked", self.upload_test_gui)
+        self.hb.pack_end(button)
+
+        # JScon edit
+        button = Gtk.Button()
+        icon = Gio.ThemedIcon(name="accessories-text-editor-symbolic")
+        image = Gtk.Image.new_from_gicon(icon, Gtk.IconSize.BUTTON)
+        button.add(image)
+        button.set_tooltip_text("Click to see the test data")
+        button.connect("clicked", self.show_test_gui)
+        self.hb.pack_end(button)
+
+        # The file chooser
+        self.btnData = Gtk.FileChooserButton()
+        self.btnData.connect("file-set", self.on_file_set)
+        if len(options.files) > 0 :
+            ifile = Path(options.files[0]).expanduser().resolve().as_posix()
+            self.btnData.set_filename(ifile)
+            self.on_file_set()
+
+        # the folder option
+        self.btnFolder = Gtk.FileChooserButton()
+        self.btnFolder.set_action(Gtk.FileChooserAction.SELECT_FOLDER)
+        self.btnFolder.connect("file-set", self.on_folder_set)
+        if options.folder and len(options.folder) > 0 :
+            ifile = Path(options.folder).expanduser().resolve().as_posix()
+            self.btnFolder.set_filename(ifile)
+
+        # The Serial number
+        self.SN = itkdb_gtk.dbGtkUtils.TextEntry()
+        self.SN.connect("text-changed", self.on_SN_changed)
+        if options.SN:
+            self.on_SN_changed(self.SN.entry, options.SN)
+
+        # The prefix
+        self.prefix = Gtk.Entry()
+        if options.prefix:
+            self.SN.set_text(options.prefix)
+
+        self.desy = Gtk.Switch()
+        self.desy.props.halign = Gtk.Align.START
+
+        self.back = Gtk.Switch()
+        self.back.props.halign = Gtk.Align.START
+        self.back.connect("state_set", self.change_to_back)
+
+        self.run = Gtk.Button(label="Run")
+        self.run.connect("clicked", self.run_analysis)
+
+        self.btn_state = Gtk.Button(label="Undef")
+        self.btn_state.set_name("btnState")
+        self.btn_state.connect("clicked", self.show_state)
+        self.btn_state.set_tooltip_text("If green all good. Click to see commnets and defects.")
+
+        if options.desy:
+            self.desy.set_active(True)
+
+        # Put the 3 objects in a Grid
+        grid = Gtk.Grid(column_spacing=5, row_spacing=5)
+        self.mainBox.pack_start(grid, False, True, 0)
+
+        grid.attach(Gtk.Label(label="Serial No."), 0, 0, 1, 1)
+        grid.attach(self.SN.entry, 1, 0, 1, 1)
+
+        grid.attach(self.btn_state, 2, 0, 1, 1)
+
+        grid.attach(Gtk.Label(label="DESY"), 3, 0, 1, 1)
+        grid.attach(self.desy, 4, 0, 1, 1)
+
+        grid.attach(Gtk.Label(label="Prefix"), 0, 1, 1, 1)
+        grid.attach(self.prefix, 1, 1, 1, 1)
+
+        grid.attach(Gtk.Label(label="Data File"), 0, 2, 1, 1)
+        grid.attach(self.btnData, 1, 2, 1, 1)
+
+        grid.attach(Gtk.Label(label="Back"), 2, 2, 1, 1)
+        grid.attach(self.back, 3, 2, 1, 1)
+        grid.attach(Gtk.Label(label="Front"), 4, 2, 1, 1)
+
+
+
+        grid.attach(Gtk.Label(label="Folder"), 0, 3, 1, 1)
+        grid.attach(self.btnFolder, 1, 3, 1, 1)
+
+        grid.attach(self.run, 0, 4, 5, 1)
+
+
+        self.mainBox.pack_start(self.message_panel.frame, True, True, 0)
+
+    def quit(self, *args):
+        """Quits the application."""
+        self.hide()
+        self.destroy()
+
+
+    def on_file_set(self, *args):
+        """File chosen from FileChooser."""
+        PSF = self.btnData.get_filename()
+        if PSF is None or not Path(PSF).exists():
+            itkdb_gtk.dbGtkUtils.complain("Could not find Data File", PSF, parent=self)
+            return
+
+        self.data_file = PSF
+
+    def on_folder_set(self, *args):
+        """Folder chosen."""
+        F = self.btnFolder.get_filename()
+        if F is None or not Path(F).exists():
+            itkdb_gtk.dbGtkUtils.complain("Could not find Output folder", F, parent=self)
+            return
+
+        self.folder = F
+        self.options.folder = F
+
+    def on_SN_changed(self, entry, value):
+        """New SN given. Ask in PDB,"""
+        if len(value) <= 0:
+            return None
+
+
+        obj = itkdb_gtk.ITkDButils.get_DB_component(self.session, value)
+        if obj is not None:
+            entry.set_text(obj["serialNumber"])
+            self.alternativeID = obj["alternativeIdentifier"]
+            self.change_to_back(None)
+
+        else:
+            itkdb_gtk.dbGtkUtils.complain("Invalid SN", value)
+
+    def change_to_back(self, *args):
+        """The front/back switch has changed."""
+        is_front = self.back.get_active()
+        if self.alternativeID is None:
+            return
+
+        if is_front:
+            txt = "{}-front".format(self.alternativeID)
+        else:
+            txt = "{}-back".format(self.alternativeID)
+
+        self.prefix.set_text(txt)
+
+    def check_SN(self, SN):
+        """Checks the serial number."""
+        if len(SN) <= 0:
+            return None
+
+        obj = itkdb_gtk.ITkDButils.get_DB_component(self.session, SN)
+        if obj is None:
+            return None
+
+        if self.alternativeID is None:
+            self.alternativeID = obj["alternativeIdentifier"]
+
+        self.change_to_back(None)
+        return obj["serialNumber"]
+
+    def show_state(self, *arg):
+        """Shows the status"""
+        if self.outDB is None:
+            dialog = Gtk.MessageDialog(
+                transient_for=self,
+                flags=0,
+                message_type=Gtk.MessageType.INFO,
+                buttons=Gtk.ButtonsType.OK,
+                text="State undefined",
+                )
+            dialog.format_secondary_text(
+                 "No analysis data available yet."
+                )
+            dialog.run()
+            dialog.destroy()
+            return
+
+        ndef = len(self.outDB["defects"])
+        ncomm = len(self.outDB["comments"])
+
+        if ndef+ncomm == 0:
+            dialog = Gtk.MessageDialog(
+                transient_for=self,
+                flags=0,
+                message_type=Gtk.MessageType.INFO,
+                buttons=Gtk.ButtonsType.OK,
+                text="All good",
+                )
+            dialog.format_secondary_text(
+                 "Petal core passed without problems."
+                )
+            dialog.run()
+            dialog.destroy()
+            return
+
+        msg = ""
+        if ndef:
+            msg += "Defects\n"
+        for D in self.outDB["defects"]:
+            msg += "{}: {}\n".format(D["name"], D["description"])
+
+        if ncomm:
+            msg += "Comments\n"
+            for C in self.outDB["comments"]:
+                msg += "{}\n".format(C)
+
+
+        dialog = Gtk.MessageDialog(
+                transient_for=self,
+                flags=0,
+                message_type=Gtk.MessageType.INFO,
+                buttons=Gtk.ButtonsType.OK,
+                text="Problems found",
+                )
+
+        dialog.format_secondary_text(msg)
+        dialog.run()
+        dialog.destroy()
+
+    def run_analysis(self, *args):
+        """Run metrology."""
+        if self.data_file is None:
+            itkdb_gtk.dbGtkUtils.complain("No data file set", "Select one", parent=self)
+            return
+
+        if self.desy.get_active():
+            self.options.desy = True
+
+        is_front = self.back.get_active()
+        suffix = "back"
+        if is_front:
+            suffix = "front"
+
+        self.petal_prefix = self.prefix.get_text().strip()
+        if len(self.petal_prefix) == 0:
+            self.petal_prefix = "{}-{}".format(self.alternativeID, suffix)
+            self.prefix.set_text(self.petal_prefix)
+
+        self.petal_SN = self.SN.get_text().strip()
+        if len(self.petal_SN) == 0 or self.petal_SN is None:
+            itkdb_gtk.dbGtkUtils.complain("Invalid SN", "SN: {}".format(self.petal_SN), parent=self)
+            return
+
+
+        with redirect_stdout(self.message_panel):
+            self.outDB = do_analysis(self.data_file, self.petal_prefix, self.petal_SN, self.options)
+
+        if len(self.outDB["defects"]) > 0:
+            itkdb_gtk.dbGtkUtils.set_button_color(self.btn_state, "red", "white")
+            self.btn_state.set_label("FAILED")
+        elif len(self.outDB["comments"]) > 0:
+            itkdb_gtk.dbGtkUtils.set_button_color(self.btn_state, "orange", "white")
+            self.btn_state.set_label("PROBLEMS")
+        else:
+            itkdb_gtk.dbGtkUtils.set_button_color(self.btn_state, "green", "white")
+            self.btn_state.set_label("PASSED")
+
+
+    def show_test_gui(self, *args):
+        """Show test data."""
+        if self.outDB is None:
+            return
+
+        values, rc = itkdb_gtk.dbGtkUtils.DictDialog.create_json_data_editor(self.outDB)
+        if rc == Gtk.ResponseType.OK:
+            self.outDB = values
+
+    def upload_test_gui(self, *args):
+        """Uploads test and attachments."""
+        self.upload_test()
+
+    def upload_test(self):
+        """Uploads test and attachments."""
+        if self.outDB is None:
+            return
+        uploadW = itkdb_gtk.UploadTest.UploadTest(self.session, payload=self.outDB)
+
+
+def main():
+    """Entry point."""
+    parser = ArgumentParser()
+    parser.add_argument('files', nargs='*', help="Input files")
+    parser.add_argument("--prefix", dest='prefix', default=None)
+    parser.add_argument("--SN", dest='SN', default=None)
+    parser.add_argument("--save", dest='save', action="store_true", default=False)
+    parser.add_argument("--desy", dest='desy', action="store_true", default=False)
+    parser.add_argument("--out", dest="out", default="petal_flatness.docx",
+                        type=str, help="The output fiel name")
+    parser.add_argument("--bottom-lp", dest='bLP', action=CommaSeparatedListAction, default=None,
+                        help="Bottom locking point fiducial coordinates")
+    parser.add_argument("--upper-lp", dest='uLP', action=CommaSeparatedListAction, default=None,
+                        help="upper locking point fiducials coordinates")
+
+    parser.add_argument("--title", dest="title", default=None,
+                        type=str, help="Document title")
+    parser.add_argument("--nbins", dest="nbins", default=25,
+                        type=int, help="Number of bins")
+    parser.add_argument("--folder", default=None, help="Folder to store output files. Superseeds folder in --out")
+    parser.add_argument("--locking_points", action="store_true", default=False)
+
+    # This is to convert a CMM file
+    parser.add_argument("--label", default="\\w+", help="The label to select")
+    parser.add_argument("--type", default="Punto", help="The class to select")
+
+    options = parser.parse_args()
+
+
+    # ITk PDB authentication
+    dlg = None
+    try:
+        # We use here the Gtk GUI
+        from itkdb_gtk import ITkDBlogin
+        dlg = ITkDBlogin.ITkDBlogin()
+        client = dlg.get_client()
+
+    except Exception:
+        # Login with "standard" if the above fails.
+        import itkdb
+        import getpass
+        client = itkdb.Client()
+        client.user._access_code1 = getpass.getpass("Access 1: ")
+        client.user._access_code2 = getpass.getpass("Access 2: ")
+        client.user.authenticate()
+        print("Hello {} !".format(client.user.name))
+
+    CM = CoreMetrology(options, session=client, title="Petal core metrology")
+    CM.write_message("Welcome !\n")
+    CM.connect("destroy", Gtk.main_quit)
+
+    CM.show_all()
+    try:
+        Gtk.main()
+
+    except KeyboardInterrupt:
+        print("Arrrgggg!!!")
+
+
+    try:
+        dlg.die()
+
+    except Exception:
+        print("Bye !")
+
+if __name__ == "__main__":
+    main()

petal_qc/metrology/data2csv.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+"""Convert IFIC raw data to CVS."""
+import io
+from metrology.convert_mitutoyo import mitutoyo2cvs
+import matplotlib.pyplot as plt
+import numpy as np
+
+def data2cvs(ifile, options):
+    """Read CMM file and convert to CSV.
+
+    Args:
+        ifile: Input file path
+        options: Program options
+
+    """
+    ofiles = []
+    odata = io.StringIO()
+    mitutoyo2cvs(ifile, odata, r"Punto[-|Vision-]\w", "Punto")
+
+    outfile = "{}-petal.csv".format(options.prefix)
+    with open(outfile, mode='w') as f:
+        f.write(odata.getvalue())
+
+    ofiles.append(outfile)
+
+    odata = io.StringIO()
+    mitutoyo2cvs(ifile, odata, "PuntoLocator", "Punto")
+
+    outfile = "{}-locators.csv".format(options.prefix)
+    with open(outfile, mode='w') as f:
+        f.write(odata.getvalue())
+
+    ofiles.append(outfile)
+    return ofiles
+
+if __name__ == "__main__":
+    import argparse
+    import sys
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('files', nargs='*', help="Input files")
+    parser.add_argument("--prefix", default="out", help="Output file")
+    parser.add_argument("--show", action="store_true", default=False)
+
+    options = parser.parse_args()
+    if len(options.files) == 0:
+        print(sys.argv[0])
+        print("I need an input file")
+        sys.exit()
+
+    ofiles = data2cvs(options.files, options)
+
+    if options.show:
+        for outfile in ofiles:
+            x, y, z = np.loadtxt(outfile, unpack=True, skiprows=1, delimiter=',')
+            fig, ax = plt.subplots(subplot_kw={'projection': '3d'})
+            surf = ax.scatter(x, y, z, c=z, marker='.', cmap=plt.cm.jet)
+            ax.set_xlabel("X")
+            ax.set_ylabel("Y")
+            ax.set_zlabel("Z")
+            fig.colorbar(surf, shrink=0.5, aspect=5, location="left")
+
+        plt.show()

petal_qc/metrology/do_Metrology.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+"""Does metrology of all files listed at input file.
+
+Examples:
+
+python3 ~/cernbox/workspace/Petal-QC/do_Metrology.py ~/Desktop/petal-metrology-files.txt
+python3 ~/cernbox/workspace/Petal-QC/do_Metrology.py --desy ~/Desktop/DESY-petal-metrology.txt
+
+"""
+import json
+import sys
+import traceback
+from argparse import Action
+from argparse import ArgumentParser
+from pathlib import Path
+import numpy as np
+from petal_qc.utils.utils import output_folder
+
+from petal_qc.metrology.PetalMetrology import petal_metrology
+
+
+class CommaSeparatedListAction(Action):
+    """Create a list from the comma sepparated numbers at imput."""
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        """The actual action."""
+        value = np.array(list(map(float, values.split(','))), dtype='float64')
+        if value.shape[0] < 3:
+            raise Exception("{} needs a 3D vector".format(self.dest))
+
+        setattr(namespace, self.dest, value)
+
+def do_analysis(fnam, prefix, SN, options):
+    """Perform analysis of a file.
+
+    Args:
+        fnam (): Input data file
+        prefix (): Prefix telling if it is front or back
+        SN (): Core serial number
+        options (): Options.
+        
+    """
+    
+    is_front = prefix.lower().find("front") >= 0
+    print(fnam, prefix)
+    options.out = prefix + '.docx'
+    options.title = prefix
+    options.is_front = is_front
+    if not hasattr(options, "SN"):
+        options.SN = ""
+
+    options.SN = SN
+    outDB = petal_metrology(fnam, options)
+
+    ofile = output_folder(options.folder, prefix + '.json')
+    with open(ofile, 'w', encoding='UTF-8') as of:
+        json.dump(outDB, of, indent=3)
+    
+    return outDB
+
+def main(ifile, options):
+    """Main entry."""
+    with open(ifile, 'r', encoding='UTF-8') as inp:
+
+        for line in inp:
+            line = line.strip()
+            if len(line) == 0:
+                continue
+
+            if line[0] == '#':
+                continue
+
+            SN = ""
+            try:
+                fnam, prefix = line.split()
+            except Exception:
+                fnam, prefix, SN, *_ = line.split()
+
+            do_analysis(fnam, prefix, SN, options)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser()
+    parser.add_argument('files', nargs='*', help="Input files")
+    parser.add_argument("--prefix", dest='prefix', default=None)
+    parser.add_argument("--SN", dest='SN', default=None)
+    parser.add_argument("--save", dest='save', action="store_true", default=False)
+    parser.add_argument("--desy", dest='desy', action="store_true", default=False)
+    parser.add_argument("--out", dest="out", default="petal_flatness.docx",
+                        type=str, help="The output fiel name")
+    parser.add_argument("--bottom-lp", dest='bLP', action=CommaSeparatedListAction, default=None,
+                        help="Bottom locking point fiducial coordinates")
+    parser.add_argument("--upper-lp", dest='uLP', action=CommaSeparatedListAction, default=None,
+                        help="upper locking point fiducials coordinates")
+
+    parser.add_argument("--title", dest="title", default=None,
+                        type=str, help="Document title")
+    parser.add_argument("--nbins", dest="nbins", default=25,
+                        type=int, help="Number of bins")
+    parser.add_argument("--folder", default=None, help="Folder to store output files. Superseeds folder in --out")
+    parser.add_argument("--locking_points", action="store_true", default=False)
+
+    # This is to convert a CMM file
+    parser.add_argument("--label", default="\\w+", help="The label to select")
+    parser.add_argument("--type", default="Punto", help="The class to select")
+
+    options = parser.parse_args()
+    if len(options.files) == 0:
+        print(sys.argv[0])
+        print("I need an input file")
+        sys.exit()
+
+    try:
+        main(options.files[0], options)
+
+    except Exception:
+        print(traceback.format_exc())