merged tacaswell/pixi

Author: FXI Operator

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -16,3 +16,6 @@ startup/calib_copy_Feb10_2019.csv
 startup/hs_err_pid7527.log
 startup/existing_plans_and_devices.yaml
 .vscode/
+# pixi environments
+.pixi/*
+!.pixi/config.toml

pixi.lock

@@ -0,0 +1,68 @@
+[workspace]
+channels = ["conda-forge"]
+name = "fxi-profile-collection"
+platforms = ["linux-64"]
+version = "2025.3.1"
+
+[system-requirements]
+libc = "2.17"
+
+[feature.profile.dependencies]
+bluesky-base = "==1.14.6"
+bluesky-queueserver = "*"
+matplotlib-base= ">=3.9.3,<4"
+networkx = ">=3.4.2,<4"
+nslsii = "==0.11.4"
+numpy = "*"
+ophyd = ">=1.11.0"
+pyepics = "*"
+python = ">=3.12,<3.13"
+semver = ">=3.0.4,<4"
+tiled-client = ">=0.1.6"
+qtpy = ">=2.4.3,<3"
+pyqt = "<6"
+reportlab = ">=4.4.1,<5"
+cytoolz = ">=1.0.1,<2"
+pypdf2 = ">=3.0.1,<4"
+scipy = ">=1.16.1,<2"
+tomopy = ">=1.14.4"
+magicgui = ">=0.10.1,<0.11"
+pystackreg = ">=0.2.8,<0.3"
+hdf5-external-filter-plugins = ">=0.1.0,<0.2"
+blosc-hdf5-plugin = ">=1.0.1,<2"
+databroker = "==2.0.0"
+epicscorelibs = ">=7.0.7.99.1.1,<8"
+bluesky-tiled-plugins = ">=2.0.0b68"
+ophyd-async = ">=0.13.7,<0.14"
+
+
+[feature.profile.pypi-dependencies]
+pvxslibs = ">=1.3.2, <2"
+
+
+[feature.qs.dependencies]
+bluesky-queueserver = "*"
+bluesky-httpserver = "*"
+
+[feature.qs.tasks]
+# This section needs some development work to understand the best way to
+# thread the required configuration through both the task and files checked into
+# the profile.  These will interact with the ansible roles for pushing out the
+# systemd units
+qs-backend = "start-re-manager --profile-dir=."
+qs-server = "uvicorn --host localhost --port 60610 bluesky_httpserver.server:app"
+
+
+[feature.terminal.dependencies]
+ipython = ">=9.5.0"
+pyside6 = "*"
+numpy = ">2"
+
+
+[feature.terminal.tasks]
+start = "unset SESSION_MANAGER PYTHONPATH && MPLBACKEND=qtagg ipython --profile-dir=."
+pvs = "ipython --profile-dir=. -c 'get_pv_types(); exit()'"
+
+[environments]
+terminal = {features=["profile", "terminal"], solve-group="profile"}
+qs = {features=["profile", "qs"], solve-group="profile"}

pixi.toml

@@ -16,7 +16,7 @@
 
 
 try:
-    from cytools import partition
+    from cytoolz import partition
 except ImportError:
     from toolz import partition
 from bluesky import plan_patterns
@@ -319,12 +319,12 @@ def fly_scan(
     @bpp.monitor_during_decorator([zps.pi_r])
     @run_decorator(md=_md)
     def fly_inner_scan():
-        
+
         for flt in filters:
             yield from mv(flt, 1)
             yield from mv(flt, 1)
         yield from bps.sleep(1)
-        
+
         # close shutter, dark images: numer=chunk_size (e.g.20)
         print("\nshutter closed, taking dark images...")
         yield from _take_dark_image(
@@ -351,7 +351,7 @@ def fly_inner_scan():
         print("\nTaking background images...")
         yield from _set_rotation_speed(rs=rot_back_velo)
         #        yield from abs_set(zps.pi_r.velocity, rs)
-        
+
         for flt in filters:
             yield from mv(flt, 1)
             yield from mv(flt, 1)
@@ -402,7 +402,7 @@ def radiography_scan(
     num_bkg=10,
     take_dark_img=True,
     relative_move_flag=1,
-    rot_first_flag=1, 
+    rot_first_flag=1,
     note="",
     simu=False,
     md=None,
@@ -579,7 +579,7 @@ def fly_scan(
         rotation speed in unit of deg/sec
 
     take_bkg_img: bool, default is True,
-        check if need to take background image (without sample)        
+        check if need to take background image (without sample)
 
     take_dark_img: bool, default is True,=True,
         check if need to take dark image (shutter closed)
@@ -603,7 +603,7 @@ def fly_scan(
     motor_y_ini = zps.sy.position
     motor_z_ini = zps.sz.position
     motor_r_ini = zps.pi_r.position
-    
+
     out_r_frac = out_r - (out_r // 360) * 360
     out_r_relative = ((target_rot_angle-1) // 360) * 360 + out_r_frac
 
@@ -623,7 +623,7 @@ def fly_scan(
 
     motor = [zps.sx, zps.sy, zps.sz, zps.pi_r]
 
-    
+
     _md = {
         "detectors": ["KinetixU"],
         "motors": [mot.name for mot in motor],
@@ -703,7 +703,7 @@ def fly_inner_scan():
         ###########################################################################
 
         rot_time = np.abs(relative_rot_angle) / np.abs(rs) + 1 # it seems acceleration/de-acceleration take more time
-        num_img = int(rot_time / true_period) 
+        num_img = int(rot_time / true_period)
 
         yield from _open_shutter(simu=simu)
         print("\nshutter opened, taking tomo images...")
@@ -957,7 +957,7 @@ def xanes_inner_scan():
                 repeat=2,
                 trans_first_flag=rot_first_flag,
             )
-        '''        
+        '''
         if len(filters):
             for filt in filters:
                 yield from mv(filt, 0)
@@ -1497,7 +1497,7 @@ def stop(self, doc):
         eng_start = plan_args["start"]
         eng_end = plan_args["stop"]
         steps = plan_args["num"]
-        try: 
+        try:
             x = plan_args['eng_list']
         except:
             x = np.linspace(eng_start, eng_end, steps)
@@ -1516,7 +1516,7 @@ def stop(self, doc):
         y0 = np.array(list(h.data(ic3.name)))
         y1 = np.array(list(h.data(ic4.name)))
         r = np.log(y0 / y1)
-        
+
         self._ax1.plot(x, y0, ".-", label=f'{ic3.name}')
         self._ax1.plot(x, y1, ".-", label=f'{ic4.name}')
         self._ax1.legend()
@@ -1916,13 +1916,13 @@ def raster_2D_scan(
     """
     !!! Note:
 
-    Filters will be inserted at all time, including: img, img_bkg, and img_dark    
-    
+    Filters will be inserted at all time, including: img, img_bkg, and img_dark
+
 
     scanning large area by moving samples at different 2D block position, defined by x_range and y_range, only work for KinetixU camera at full resolution (2048 x 2048)
     for example, set x_range=[-1,1] and y_range=[-2, 2] will totally take 3 x 5 = 15 images and stitch them together
-    
-    
+
+
     Inputs:
     -------
 
@@ -2043,7 +2043,7 @@ def raster_2D_scan(
     @run_decorator(md=_md)
     def raster_2D_inner():
         select_filters(filters)
-        
+
         # take dark image
         print("take 5 dark image")
         yield from _take_dark_image(
@@ -2126,19 +2126,19 @@ def raster_2D_scan_modify(
     scan_x_flag=1,
     flag_take_dark_img=True,
     flag_take_bkg_img=True,
-    flag_close_shutter=True,    
+    flag_close_shutter=True,
     md=None,
 ):
     """
     !!! Note:
 
-    Filters will be inserted at all time, including: img, img_bkg, and img_dark    
-    
+    Filters will be inserted at all time, including: img, img_bkg, and img_dark
+
 
     scanning large area by moving samples at different 2D block position, defined by x_range and y_range, only work for KinetixU camera at full resolution (2048 x 2048)
     for example, set x_range=[-1,1] and y_range=[-2, 2] will totally take 3 x 5 = 15 images and stitch them together
-    
-    
+
+
     Inputs:
     -------
 
@@ -2258,7 +2258,7 @@ def raster_2D_scan_modify(
     @stage_decorator(list(detectors) + motor)
     @run_decorator(md=_md)
     def raster_2D_inner():
-         
+
         # take dark image
         if flag_take_dark_img:
             print("take 5 dark image")
@@ -2348,7 +2348,7 @@ def raster_2D_scan_filter_bkg(
 
     !!! Note:
 
-    Filters will ONLY be inserted when taking background image   
+    Filters will ONLY be inserted when taking background image
 
 
     scanning large area by moving samples at different 2D block position, defined by x_range and y_range, only work for KinetixU camera at full resolution (2048 x 2048)
@@ -2609,7 +2609,7 @@ def raster_2D_scan_individal_bkg(
     global ZONE_PLATE
     motor = [zps.sx, zps.sy, zps.sz, zps.pi_r]
     detectors = [KinetixU, ic3]
-    
+
     motor_x_ini = zps.sx.position
     motor_y_ini = zps.sy.position
     motor_z_ini = zps.sz.position
@@ -3299,7 +3299,7 @@ def raster_2D_xanes2(
 ):
 
     '''
-    take 2D-xanes at defined grid position, using "multipos_2D_xanes_scan2" 
+    take 2D-xanes at defined grid position, using "multipos_2D_xanes_scan2"
     '''
 
     motor_x_ini = zps.sx.position
@@ -3814,4 +3814,3 @@ def tomo_mosaic_scan(
     txt4 = "\n######  mosaic tomogrpahy scan finished  ######"
     txt = txt1 + txt4 + txt3
     insert_text(txt)
-

startup/41-scans.py

@@ -20,13 +20,20 @@ def test_scan(
     out_r=0,
     period=0.1,
     num_img=10,
+<<<<<<< HEAD
     num_bkg=10,
     relative_move_flag=False,    
     sleep_time=0, 
     rot_first_flag=1, 
+=======
+    #num_bkg=10,
+    relative_move_flag=False,
+    sleep_time=0,
+    rot_first_flag=1,
+>>>>>>> tacaswell/pixi
     close_shutter_in_scan=False,
     note="",
-    
+
     simu=False,
     md=None,
 ):
@@ -140,7 +147,7 @@ def inner_scan():
         '''
         yield from mv(zps.pi_r, r_out)
         yield from mv(zps.sz, z_out)
-        yield from mv(zps.sx, x_out, zps.sy, y_out)        
+        yield from mv(zps.sx, x_out, zps.sy, y_out)
         for i in range(num_bkg):
             yield from trigger_and_read(list(detectors))
         '''
@@ -153,7 +160,7 @@ def inner_scan():
         # close shutter, taking dark image
         yield from _close_shutter(simu=simu)
         '''
-        
+
         print('move sample back to initial position')
         yield from _move_sample_in(
             motor_x_ini,
@@ -192,7 +199,7 @@ def test_scan2(
     take_dark_img=True,
     take_bkg_img=True,
     relative_move_flag=1,
-    rot_first_flag=1, 
+    rot_first_flag=1,
     close_shutter_at_end=True,
     note="",
     simu=False,
@@ -303,7 +310,7 @@ def inner_scan():
         yield from _take_image(detectors, motors, num=1, stream_name="primary")
         if close_shutter_at_end:
             yield from _close_shutter(simu=simu)
-        
+
 
     uid = yield from inner_scan()
     yield from mv(KinetixU.cam.image_mode, 2)
@@ -365,12 +372,12 @@ def z_scan(
         x_out = x_ini + out_x if not (out_x is None) else x_ini
         y_out = y_ini + out_y if not (out_y is None) else y_ini
         z_out = z_ini + out_z if not (out_z is None) else z_ini
-        
+
     else:
         x_out = out_x if not (out_x is None) else x_ini
         y_out = out_y if not (out_y is None) else y_ini
         z_out = out_z if not (out_z is None) else z_ini
-        
+
 
     if scan_motor == 'zp_x':
         zp_ini = zp.x.position  # zp.x intial position
@@ -970,7 +977,7 @@ def load_cell_scan(
             pos_list = pbsl_y_pos_list[::-1]
         else:
             pos_list = pbsl_y_pos_list.copy()
-        idx += 1 
+        idx += 1
         for pbsl_pos in pos_list:
             yield from mv(pbsl.y_ctr, pbsl_pos)
             for i in range(num):
@@ -1135,7 +1142,7 @@ def beam_profile_scan(
         mot = pbsl.y_ctr
     elif dir == 'x':
         pbsl_ctr_ini = pbsl.x_ctr.position
-        mot = pbsl.x_ctr   
+        mot = pbsl.x_ctr
 
     pbsl_pos_list = np.linspace(start, end, steps, endpoint=True)
     num_pbsl_pos = steps
@@ -1591,7 +1598,7 @@ def knife_edge_scan_for_condensor(
     from numpy import polyfit, poly1d
     from scipy.optimize import curve_fit, least_squares
     from scipy.special import erf
-    from scipy.signal import gaussian
+    from scipy.signal.windows import gaussian
 
     yield from rel_grid_scan(
         det,