Safety Z home and CSV files created

A Z homing safety (G28 Z) code was added and now the printer starts its gohome function by homing Z before the other axes. Many CSV files were created and already have the placeholders for the predicted positions. The main code was updated to implement some of the CSV-based positions

alab_control/SEM_autoprep/Positions/disks_tray_clean.csv

@@ -0,0 +1,13 @@
+CDISK1,23.8,173.8,None
+CDISK2,23.8,173.8,None
+CDISK3,23.8,173.8,None
+CDISK4,23.8,173.8,None
+CDISK5,23.8,173.8,None
+CDISK6,23.8,173.8,None
+CDISK7,23.8,173.8,None
+CDISK8,23.8,173.8,None
+CDISK9,23.8,173.8,None
+CDISK10,23.8,173.8,None
+CDTRAY_Z1,None,None,133
+CDTRAY_Z2,None,None,141.5
+CDTRAY_Z3,None,None,137

alab_control/SEM_autoprep/Positions/disks_tray_used.csv

@@ -0,0 +1,13 @@
+UDISK1,23.8,173.8,None
+UDISK2,23.8,173.8,None
+UDISK3,23.8,173.8,None
+UDISK4,23.8,173.8,None
+UDISK5,23.8,173.8,None
+UDISK6,23.8,173.8,None
+UDISK7,23.8,173.8,None
+UDISK8,23.8,173.8,None
+UDISK9,23.8,173.8,None
+UDISK10,23.8,173.8,None
+UDTRAY_Z1,None,None,133
+UDTRAY_Z2,None,None,141.5
+UDTRAY_Z3,None,None,137

alab_control/SEM_autoprep/Positions/equipment.csv

@@ -0,0 +1,10 @@
+ROTATOR_A,23.8,173.8,None
+ROTATOR_B,23.8,173.8,None
+ROTATOR_C,23.8,173.8,None
+ROTATOR_D,23.8,173.8,None
+CHARGER,23.8,173.8,None
+CHARGER_Z1,23.8,173.8,None
+CHARGER_Z2,23.8,173.8,None
+LASER,23.8,173.8,None
+LASER_Z1,23.8,173.8,None
+LASER_Z2,23.8,173.8,None

alab_control/SEM_autoprep/Positions/intermediate_positions.csv

@@ -0,0 +1 @@
+HOME,20,20,20

alab_control/SEM_autoprep/Positions/phenom_handler.csv

@@ -0,0 +1,5 @@
+PH_OPENED,23.8,173.8,None
+PH_CLOSED,23.8,173.8,None
+PH_L1,23.8,173.8,None
+PH_L2,23.8,173.8,None
+PH_L3,23.8,173.8,None

alab_control/SEM_autoprep/Positions/phenom_stubs.csv

@@ -0,0 +1,18 @@
+PH_STUB1,23.8,173.8,None
+PH_STUB2,23.8,173.8,None
+PH_STUB3,23.8,173.8,None
+PH_STUB4,23.8,173.8,None
+PH_STUB5,23.8,173.8,None
+PH_STUB6,23.8,173.8,None
+PH_STUB7,23.8,173.8,None
+PH_STUB8,23.8,173.8,None
+PH_STUB9,23.8,173.8,None
+PH_STUB10,23.8,173.8,None
+PH_STUB11,23.8,173.8,None
+PH_STUB12,23.8,173.8,None
+PH_STUB13,23.8,173.8,None
+PH_STUB14,23.8,173.8,None
+PH_STUB15,23.8,173.8,None
+PH_Z1,None,None,133
+PH_Z2,None,None,141.5
+PH_Z3,None,None,137

alab_control/SEM_autoprep/Positions/stubs_tray.csv

@@ -0,0 +1,21 @@
+TSTUB1,23.8,173.8,None
+TSTUB2,23.8,173.8,None
+TSTUB3,23.8,173.8,None
+TSTUB4,23.8,173.8,None
+TSTUB5,23.8,173.8,None
+TSTUB6,23.8,173.8,None
+TSTUB7,23.8,173.8,None
+TSTUB8,23.8,173.8,None
+TSTUB9,23.8,173.8,None
+TSTUB10,23.8,173.8,None
+TSTUB11,23.8,173.8,None
+TSTUB12,23.8,173.8,None
+TSTUB13,23.8,173.8,None
+TSTUB14,23.8,173.8,None
+TSTUB15,23.8,173.8,None
+TSTUB16,23.8,173.8,None
+TSTUB17,23.8,173.8,None
+TSTUB18,23.8,173.8,None
+STRAY_Z1,None,None,133
+STRAY_Z2,None,None,141.5
+STRAY_Z3,None,None,137

alab_control/SEM_autoprep/Tests/csv_helper.py

@@ -15,7 +15,6 @@ def read_CSV_into_positions(path=CWD + '\\alab_control\\SEM_autoprep\\Tests\\Sam
     for lines in csvFile:
       #Each line has a list of 4 arguments, argument 0 is the name of the position, and argument 1, 2, 3 correspond to x, y, z, respectively
       positions[lines[0]] = ((float_or_none(lines[1]), float_or_none(lines[2]), float_or_none(lines[3])))
-
   return positions
 
 

alab_control/SEM_autoprep/Tests/stubs.csv

@@ -0,0 +1,21 @@
+BCP1,90,120,60
+BCP2,90,120,60
+BCP3,90,120,60
+BCP4,90,120,60
+HOME,90,120,60
+REST,15,15,15
+STUB1,23.8,173.8,None
+STUB2,23.8,173.8,None
+STUB3,23.8,173.8,None
+STUB4,23.8,173.8,None
+STUB5,23.8,173.8,None
+STUB6,23.8,173.8,None
+STUB7,23.8,173.8,None
+STUB8,23.8,173.8,None
+STUB9,23.8,173.8,None
+STUB10,23.8,173.8,None
+STUB11,23.8,173.8,None
+STUB12,23.8,173.8,None
+STUB13,23.8,173.8,None
+STUB14,23.8,173.8,None
+STUB15,23.8,173.8,None

alab_control/SEM_autoprep/csv_helper.py

@@ -0,0 +1,20 @@
+import csv
+import os
+CWD = os.getcwd()
+positions = {}
+
+def float_or_none(s):
+  if s == 'None':
+    return None
+  return float(s)
+
+
+def read_CSV_into_positions(path=CWD + '\\alab_control\\SEM_autoprep\\Tests\\SampleFile.csv'):
+  with open(path, mode ='r') as file:
+    csvFile = csv.reader(file)
+    for lines in csvFile:
+      #Each line has a list of 4 arguments, argument 0 is the name of the position, and argument 1, 2, 3 correspond to x, y, z, respectively
+      positions[lines[0]] = ((float_or_none(lines[1]), float_or_none(lines[2]), float_or_none(lines[3])))
+  return positions
+
+

alab_control/SEM_autoprep/sample_prep.py

@@ -1,11 +1,18 @@
 from alab_control.ender3 import Ender3
-from alab_control.SEM_autoprep.Tests import csv_helper
+from alab_control.SEM_autoprep import csv_helper
 #from ender3 import Ender3
 import serial
 import os
 
 CWD = os.getcwd()
-path = CWD + '\\alab_control\\SEM_autoprep\\Tests\\SampleFile.csv'
+path = CWD + '\\alab_control\\SEM_autoprep\\Positions\\'
+clean_disks_filename = 'disks_tray_clean.csv'
+used_disks_filename = 'disks_tray_used.csv'
+equipment_filename = 'equipment.csv'
+intermediate_positions_filename = 'intermediate_positions.csv'
+phenom_holder_positions_filename = 'phenom_stubs.csv'
+phenom_handler_filename = 'phenom_handler.csv'
+stubs_tray_filename = 'stubs_tray.csv'
 
 class SamplePrepEnder3(Ender3):
     """This class is for controlling the Ender3 3D printer for sample preparation."""
@@ -14,7 +21,13 @@ class SamplePrepEnder3(Ender3):
     CRUCIBLE_HEIGHT = 39
 
     # positions
-    positions = csv_helper.read_CSV_into_positions(path)
+    clean_disk_pos = csv_helper.read_CSV_into_positions(path + clean_disks_filename)
+    used_disk_pos = csv_helper.read_CSV_into_positions(path + used_disks_filename)
+    equipment_pos = csv_helper.read_CSV_into_positions(path + equipment_filename)
+    intermediate_pos = csv_helper.read_CSV_into_positions(path + intermediate_positions_filename)
+    used_stub_pos = csv_helper.read_CSV_into_positions(path + phenom_holder_positions_filename)
+    phenom_handler_pos = csv_helper.read_CSV_into_positions(path + phenom_handler_filename)
+    clean_stub_pos = csv_helper.read_CSV_into_positions(path + stubs_tray_filename)
 
 
 if __name__ == "__main__":
@@ -25,9 +38,6 @@ class SamplePrepEnder3(Ender3):
     print(
         "**************************************************************************** \n "
     )
-    print(
-        "The following lines show your COM ports.\nPlease select your MAPPLE printer by typing its number: \n"
-    )
 
     try:
         r = SamplePrepEnder3("COM3") 
@@ -37,14 +47,15 @@ class SamplePrepEnder3(Ender3):
         ports = list(serial.tools.list_ports.comports())
         for p in ports:
             print(p)
-        input("\n Press enter to end the program.")
+        input("\n Edit the source code to match the MAPLE COM port. Press enter to end the program.")
         exit()
 
     print("Printer is resetting the positioning system. Please wait... \n")
     r.gohome()
 
+
     print("Homing head unit. Please wait...")
-    r.moveto(*r.positions["HOME"])
+    r.moveto(*r.intermediate_pos["HOME"])
     r.speed = 0.5
     print("Done.")
 
@@ -65,34 +76,35 @@ class SamplePrepEnder3(Ender3):
 
         while True:
             # Ask the user to choose part 1 or part 2
-            stub_choice = input("Please enter 1 for Stub 1 or 2 for Stub 2: ")
-            r.moveto(x=35, y=173.8, z=60)
-            r.moveto(z=115)
-            pump_confirm = input("Please turn on vacuum pump and press enter.")
+            stub_choice = input("Please enter the number of the stub you want to pick:")
+
 
             try:
                 int(stub_choice)
-                r.moveto(*r.positions["STUB" + stub_choice])
+                #r.moveto(x=35, y=173.8, z=60)
+                r.moveto(*r.clean_stub_pos["TSTUB" + stub_choice])
+                #r.moveto(z=115)
+                pump_confirm = input("Please turn on vacuum pump and press enter.")
                 break
             except Exception:
                 print("Invalid choice. Please try again.")
 
-        r.moveto(z=133)
+        r.moveto(*r.clean_stub_pos["STRAY_Z1"])
 
         r.speed = 0.005
-        r.moveto(z=141.5)
+        r.moveto(*r.clean_stub_pos["STRAY_Z2"])
 
-        r.moveto(z=137)
+        r.moveto(*r.clean_stub_pos["STRAY_Z3"])
 
         while True:
             picked_confirm = input(
-                "Stub picked? C to continue, R to try again, M for manual, A to abort."
+                "Stub picked? C to continue, R to try again, M for manual, A to abort." # abort not available yet
             )
-            if picked_confirm.lower() == "c":  # abort not available yet
+            if picked_confirm.lower() == "c":  
                 break
             elif picked_confirm.lower() == "r":
-                r.moveto(z=141.5)
-                r.moveto(z=137)
+                r.moveto(*r.clean_stub_pos["STRAY_Z2"])
+                r.moveto(*r.clean_stub_pos["STRAY_Z3"])
                 picked_confirm = input(
                     "Stub picked? If not, R to try again, C to continue."
                 )
@@ -128,12 +140,7 @@ class SamplePrepEnder3(Ender3):
         exp_confirm = input("Please press enter when the exposing is finished.")
         r.moveto(z=60)
 
-        if stub_choice == "1":
-            r.moveto(x=23.8, y=173.8)
-        elif stub_choice == "2":
-            r.moveto(x=23.8, y=173.8)
-        else:
-            print("Invalid choice. Please try again.")
+        r.moveto(*r.stub_positions["STUB" + stub_choice])
 
         r.moveto(z=137)
         r.speed = 0.005

alab_control/_base_gcode_robot.py

@@ -122,6 +122,7 @@ def moveto(
             zhop (bool): Whether to z-hop (raise the z-axis) before moving to the target position. This is useful to avoid collisions.
         """
         x, y, z = self.check_move_is_valid(x, y, z)  # check for invalid move
+        print("Moving to " + str((x, y, z)))
         if (x == self.position[0]) and (y == self.position[1]):
             zhop = False  # turn off zhopping if we're not moving in x or y
 
@@ -174,6 +175,7 @@ def get_current_position(self) -> None:
 
     def gohome(self) -> None:
         """Homes the robt (calls the G28 command) and updates the position."""
+        self.write("G28 Z")
         self.write("G28 X Y Z")
         self.get_current_position()