Only allow flat correction if not existing

cockpit

@@ -3,6 +3,7 @@
 import os
 import re
 import json
+import glob
 import shlex
 import collections
 import datetime
@@ -45,6 +46,16 @@ def extract_motor_positions(id19_header):
     return {k: float(v) for (k, v) in zip(names, values)}
 
 
+def have_flats(path):
+    large = os.path.join(path, 'fc')
+    small = os.path.join(path, 'fc-small')
+
+    return (os.path.exists(large) and
+            os.path.exists(small) and
+            glob.glob(os.path.join(large, '*.tif')) and
+            glob.glob(os.path.join(small, '*.tif')))
+
+
 class Configuration(object):
 
     def __init__(self, source, destination):
@@ -279,8 +290,6 @@ class Application(object):
         info = self.read_info()
         axis = (float(info['Col_end']) + 1) / 2.0
         axis_step = 0.25
-        axis_start = axis - slices_per_device * axis_step
-        axis_stop = axis + slices_per_device * axis_step
 
         fname = os.path.join(self.config.destination, '{}0000.edf'.format(self.prefix))
         header = read_edf_id19_header(fname)
@@ -300,8 +309,12 @@ class Application(object):
             x_region /= 2
             y_region /= 2
             axis /= 2
+            axis_step /= 2
             fc_path = '{prefix}/fc-small'.format(prefix=self.prefix)
 
+        axis_start = axis - slices_per_device * axis_step
+        axis_stop = axis + slices_per_device * axis_step
+
         self.log.info(" Using theta = {}, inclination angle = {}".format(theta, inclination_angle))
         self.log.info(" Scanning lamino angle within [{}:{}:{}]".format(angle_start, angle_stop, angle_step))
         self.log.info(" Scanning x axis within [{}:{}:{}]".format(axis_start, axis_stop, axis_step))
@@ -325,8 +338,8 @@ class Application(object):
                ' {fc_path}'
                ' {opt_params}'
                ' --reco-params "{params}"'
-               ' --params-filename params.json'
-               .format(opt_params=opt_params, params=params, fc_path=fc_path))
+               ' --params-filename {prefix}/params.json'
+               .format(opt_params=opt_params, params=params, fc_path=fc_path, prefix=self.prefix))
 
         return self.run_command(cmd)
 
@@ -373,7 +386,7 @@ class Application(object):
         self.log.highlight("Quick optimization ...")
 
         if self.optimize(True):
-            with open('params.json') as f:
+            with open(os.path.join(self.prefix, 'params.json')) as f:
                 opt = json.load(f)
                 self.log.highlight(" Optimal axis: {}".format(opt['lamino-angle']['value']))
                 self.log.highlight(" Optimal center: {}".format(opt['x-center']['value'] * 2.0))
@@ -386,7 +399,7 @@ class Application(object):
         self.log.highlight("Optimizing ...")
 
         if self.optimize(False):
-            with open('params.json') as f:
+            with open(os.path.join(self.prefix, 'params.json')) as f:
                 opt = json.load(f)
                 self.log.highlight(" Optimal axis: {}".format(opt['lamino-angle']['value']))
                 self.log.highlight(" Optimal center: {}".format(opt['x-center']['value']))
@@ -419,25 +432,19 @@ class Application(object):
 
         quit = Action('e', 'Exit', self.on_quit, machine.QUIT)
         sync = Action('s', 'Sync', self.on_sync, machine.SYNC)
-        flatcorrect = Action('f', 'Flat correct', self.on_flat_correct, machine.FLATCORRECT)
         clean = Action('c', 'Clean', self.on_clean, machine.CLEAN)
         quick_optimize = Action('q', 'Quick', self.on_quick_optimize, machine.QUICK_OPTIMIZE)
         optimize = Action('o', 'Optimize', self.on_optimize, machine.OPTIMIZE)
 
         machine.add_action(machine.START, sync)
-        machine.add_action(machine.START, flatcorrect)
         machine.add_action(machine.START, quick_optimize)
         machine.add_action(machine.START, optimize)
         machine.add_action(machine.START, quit)
 
-        machine.add_action(machine.SYNC, flatcorrect)
         machine.add_action(machine.SYNC, quit)
 
-        machine.add_action(machine.FLATCORRECT, quick_optimize)
-        machine.add_action(machine.FLATCORRECT, optimize)
-        machine.add_action(machine.FLATCORRECT, quit)
-
         machine.add_action(machine.QUICK_OPTIMIZE, sync)
+        machine.add_action(machine.QUICK_OPTIMIZE, optimize)
         machine.add_action(machine.QUICK_OPTIMIZE, quit)
 
         machine.add_action(machine.OPTIMIZE, sync)
@@ -446,6 +453,14 @@ class Application(object):
         machine.add_action(machine.CLEAN, sync)
         machine.add_action(machine.CLEAN, quit)
 
+        if not have_flats(self.config.destination):
+            flatcorrect = Action('f', 'Flat correct', self.on_flat_correct, machine.FLATCORRECT)
+            machine.add_action(machine.START, flatcorrect)
+            machine.add_action(machine.SYNC, flatcorrect)
+            machine.add_action(machine.FLATCORRECT, quick_optimize)
+            machine.add_action(machine.FLATCORRECT, optimize)
+            machine.add_action(machine.FLATCORRECT, quit)
+
         cmd_window.set_actions(machine.actions)
 
         self.log = LogList(right_pane, colors)